Herbicide resistance gene, compositions and methods

ABSTRACT

The present disclosure provides methods, recombinant DNA molecules, recombinant host cells containing the DNA molecules, and transgenic and genetically engineered plant cells, plant tissue, seeds and plants which contain and express an herbicide resistant protoporphyrinogen oxidase such that they germinate from seed and grow in the presence of an amount of herbicide where the parent plant does not. Such plants are especially appropriate for use in agriculture or horticulture where herbicides are used to kill undesirable plants which might contaminate or compete with the transgenic plant of interest.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation-in-Part of U.S. application Ser. No. 11/466,662, filed Aug. 23, 2006, which application claims benefit of U.S. Provisional Application 60/807,780 filed Jul. 19, 2006 and of U.S. Provisional Application 60/711,204 filed Aug. 25, 2005; all of said applications are incorporated by reference herein to the extent there is no inconsistency with the present disclosure.

ACKNOWLEDGEMENT OF FEDERAL RESEARCH SUPPORT

Not applicable

BACKGROUND OF THE INVENTION

The field of the present invention is plant molecular biology, especially as related to genetically modified plants with resistance to herbicide. Specifically, the present invention relates to transgenic plants in which herbicide resistance is achieved by introducing a coding sequence which determines an herbicide resistance protoporphyrinogen oxidase (PPO) which is expressed in chloroplasts and mitochondria. Such transgenic crop plants are useful in fields where it is desired to spray herbicide to improve crop yield.

A major concern with the use of herbicides for weed control is the selection of resistant populations. To date, over 300 different herbicide-resistant weed biotypes have been identified worldwide (see weedscience.com on the internet). Numerous factors influence the likelihood of herbicide-resistance evolution in a weed population, and certain herbicides are more prone to resistance evolution than are others. For example, populations of 95 weed species have been reported with resistance to herbicides that inhibit acetolactate synthase (ALS), whereas evolved resistance to herbicides that inhibit protoporphyrinogen oxidase (PPO) has been reported for only three weeds (weedscience.com website), even though these herbicides were first commercialized in the 1960s (1). The first weed to evolve resistance to PPO inhibitors was Amaranthus tuberculatus (waterhemp), an increasingly problematic weed of agronomic production systems throughout the Midwestern United States.

The biosynthetic pathways which lead to the production of chlorophyll and heme share a number of common steps. Chlorophyll is a light harvesting pigment present in all green photosynthetic organisms. Heme is a cofactor of hemoglobin, cytochromes, P450 mixed-function oxygenases, peroxidases, and catalases (see, e.g. Lehninger, 1975, Biochemistry. Worth Publishers, New York), and is therefore a necessary component for all aerobic organisms. The last common step in chlorophyll and heme biosynthesis is the oxidation of protoporphyrinogen IX to protoporphyrin IX. Protoporphyrinogen oxidase (referred to herein as PPO or protox) is the enzyme which catalyzes this last oxidation step (Matringe et al. 1989. Biochem. J. 260: 231).

An approach that has been used to isolate biosynthetic genes in metabolic pathways from organisms including the higher eukaryotes is the complementation of microbial (auxotrophic) mutants deficient in the activity of interest. For this approach, a library of cDNAs from the higher eukaryote is cloned in a vector that can direct expression of the cDNA in the microbial host. The vector is then transformed or otherwise introduced into the mutant, and colonies are selected that no longer require the nutritional supplementation of interest. Microbial mutants believed defective in PPO activity have been described (e.g. E. coli (Sasarman et al. 1979. J. Gen. Microbiol. 113: 297), Salmonella typhimurium (Xu et al. 1992. J. Bacteriol. 174: 3953), and Saccharomyces cerevisiae (Camadro et al. 1982. Biochem. Biophys. Res. Comm. 106: 724.

The use of herbicides to control undesirable vegetation such as weeds or plants in crops has become common, with the relevant market exceeding a billion dollars a year. Despite extensive herbicide use, weed control remains a significant and costly problem for farmers. Since various weed species are resistant to herbicides, the production of effective herbicides becomes increasingly important, as is the development of agronomically important plants which are resistant to one or more herbicides.

The PPO enzyme is the target of a variety of herbicides. PPO-inhibiting herbicides include many different structural classes of molecules (Duke et al. 1991. Weed Sci. 39: 465; Nandihalli et al. 1992. Pesticide Biochem. Physiol. 43: 193; Matringe et al. 1989. FEBS Lett. 245: 35; Yanase and Andoh. 1989. Pesticide Biochem. Physiol. 35: 70). These herbicidal compounds include the diphenylethers {e.g. lactofen, (±)-2-ethoxy-1-methyl-2-oxoethyl 5-{2-chloro-4-(trifluoromethyl)phenoxy}-2-nitrobenzoate; acifluorfen, 5-{2-chloro-4-(trifluoromethyl)phenoxy}-2-nitrobezoic acid; its methyl ester; or oxyfluorfen, 2-chloro-1-(3-ethoxy-4-nitrophenoxy)-4-(trifluorobenzene)}, oxidiazoles, (e.g. oxidiazon, 3-{2,4-dichloro-5-(1-methylethoxy)phenyl}-5-(1,1-dimethylethyl)-1,3,4-oxadiazol-2-(3H)-one), cyclic imides (e.g. S-23142, N-(4-chloro-2-fluoro-5-propargyloxyphenyl)-3,4,5,6-tetrahydrophthalimide; chlorophthalim, N-(4-chlorophenyl)-3,4,5,6-tetrahydrophthalimide), phenyl pyrazoles (e.g. TNPP-ethyl, ethyl 2-{1-(2,3,4-trichlorophenyl)-4-nitropyrazolyl-5-oxy}propionate; M&B 39279), pyridine derivatives (e.g. LS 82-556), and phenopylate and its O-phenylpyrrolidino- and piperidinocarbamate analogs. Many of these compounds competitively inhibit the normal reaction catalyzed by the enzyme, apparently acting as substrate analogs.

Additional herbicides of interest include 3-Phenyluracils of formula I

wherein R¹ is methyl or NH₂; R² is C₁-C₂-haloalkyl; R³ is hydrogen or halogen; R⁴ is halogen or cyano; R⁵ is hydrogen, cyano, C₁-C₆-alkyl, C₁-C₆-alkoxy, C₁-C₄-alkoxy-C₁-C₄-alkyl, C₃-C₇-cycloalkyl, C₃-C₆-alkenyl, C₃-C₆-alkynyl or benzyl which is unsubstituted or substituted by halogen or alkyl; and R⁶, R⁷ independently of one another are hydrogen, C₁-C₆-alkyl, C₁-C₆-alkoxy, C₃-C₆-alkenyl, C₃-C₆-alkynyl, C₃-C₇-cycloalkyl, C₃-C₇-cycloalkenyl, phenyl or benzyl, where each of the 8 abovementioned substituents is unsubstituted or may be substituted by 1 to 6 halogen atoms and/or by one, two or three groups selected from: OH, NH₂, CN, CONH₂, C₁-C₄-alkoxy, C₁-C₄-haloalkoxy, C₁-C₄-alkylthio, C₁-C₄-haloalkylthio, C₁-C₄-alkylsulfonyl, C₁-C₄-haloalkylsulfonyl, C₁-C₄-alkylamino, di(C₁-C₄-alkyl)amino, formyl, C₁-C₄-alkylcarbonyl, C₁-C₄-alkoxycarbonyl, C₁-C₄-alkylaminocarbonyl, di(C₁-C₄-alkyl)aminocarbonyl, C₃-C₇-cycloalkyl, phenyl and benzyl; or R⁶, R⁷ together with the nitrogen atom form a 3-, 4-, 5-, 6- or 7-membered saturated or unsaturated nitrogen heterocycle which may be substituted by 1 to 6 methyl groups and which may contain 1 or 2 further heteroatoms selected from the group consisting of nitrogen, oxygen and sulfur as ring members, and their agriculturally acceptable salts (as described in the patent application PCT/EP 01/04850.

Application of PPO-inhibiting herbicides results in the accumulation of protoporphyrinogen IX in the chloroplast and mitochondria, which is believed to leak into the cytosol where it is oxidized by a peroxidase. When exposed to light, protoporphyrin IX causes formation of singlet oxygen in the cytosol and the formation of other reactive oxygen species, which can cause lipid peroxidation and membrane disruption leading to rapid cell death (Lee et al. 1993. Plant Physiol. 102: 881).

Not all PPO enzymes are sensitive to herbicides which inhibit plant PPO enzymes. Both the Escherichia coli and Bacillus subtilis PPO enzymes (Sasarmen et al. 1993. Can. J. Microbiol. 39: 1155; Dailey et al. 1994. J. Biol. Chem. 269: 813) are resistant to these herbicidal inhibitors. Mutants of the unicellular alga Chlamydomonas reinhardtii resistant to the phenylimide herbicide S-23142 have been reported (Kataoka et al. 1990. J. Pesticide Sci. 15: 449; Shibata et al. 1992. In Research in Photosynthesis, Vol. III, N. Murata, ed. Kluwer: Netherlands. pp. 567-70). At least one of these mutants appears to have an altered PPO activity that is resistant not only to the herbicidal inhibitor on which the mutant was selected, but also to other classes of protox inhibitors (Oshio et al. 1993. Z. Naturforsch. 48c: 339; Sato et al. 1994. In ACS Symposium on Porphyric Pesticides, S. Duke, ed. ACS Press: Washington, D.C.). A mutant tobacco cell line has also been reported that is resistant to the inhibitor S-21432 (Che et al. 1993. Z. Naturforsch. 48c: 350). Auxotrophic E. coli mutants have been used to confirm the herbicide resistance of cloned plant PPOs.

There is a need in the art for effective and efficient herbicide resistance genes in plants, especially crop plants, so that application of herbicide to cultivated fields results in good growth of the desired crop plants and eradication (or significant reduction) in pest plants, as well as for selectable markers for transgenic plants, plant cells and plant tissue.

SUMMARY OF THE INVENTION

The present invention provides a DNA construct comprising coding sequence for an herbicide resistant protoporphyrinogen oxidase (PPO) enzyme operably linked to a transcription regulatory sequence, especially one from a plant, and advantageously, a strong constitutive transcription regulatory sequence from a plant. A consensus sequence of an herbicide resistant PPO coding sequence is derived from Amaranthus tuberculatus and is presented in SEQ ID NO:13, and the consensus amino acid sequence is given in SEQ ID NO:14. Specifically exemplified sequences isolated from herbicide resistant A. tuberculatus are disclosed herein; see also SEQ ID NOs:13 and 14, 25 and 26, 29 and 30, and 45 and 46. The wild type (herbicide sensitive) A. tuberculatus coding and protein sequences are shown in SEQ ID NO:15 and SEQ ID NO:16; other herbicide-sensitive PPXL2 sequences are given in SEQ ID NOs: 21-22 and 27-28. Also within the scope of this invention are isolated nucleic acid molecules and vectors (plasmid or virus) comprising the herbicide resistant PPO coding sequences of the present invention, advantageously operably linked to transcription regulatory sequences. The critical feature of an herbicide resistant PPO enzyme of the present invention is a deletion of a glycine residue at amino acid 210 or 211, with reference to SEQ ID NO:16. See also FIG. 10B for various amino acid sequence polymorphisms that can be present in the Glycine210 deleted PPO, without loss of either enzymatic function or herbicide resistance. It is understood that there can be limited sequence variation from the specifically exemplified herbicide resistant sequences or consensus sequences, provided that the glycine deletion at a position corresponding to or aligned with position 210 or 211 of SEQ ID NO:16 is maintained, especially where there are from one to five amino acid substitutions, deletions or insertions and where the enzymatic activity and herbicide resistance of the enzyme is not eliminated.

Plants expressing the herbicide resistant PPX2L proteins or an equivalent herbicide resistant protein having the noted glycine (or functionally equivalent amino acid) deletion of the present invention are believed to be significantly improved in resistance over certain prior art herbicide resistant PPX2L proteins. In contrast to the corresponding wild type PPO, the resistant PPO of the present invention exhibits reduced sensitivity to PPO-inhibiting herbicides including lactofen, acifluorfen, flumiclorac, fomesafen, flumioxazin, and sulfentrazone. All synonymous sequences encoding the resistant PPO described herein are encompassed by the present invention.

Provided herein are recombinant plant cells, recombinant plant tissue, transgenic plants (including transgenic progeny plants) and transgenic plant seed which contain the DNA constructs of the present invention. Transgenic plants which contain the DNA construct are resistant to killing and/or growth inhibition by protoporphyrinogen-IX oxidase-inhibiting herbicides including, but not limited to, lactofen, acifluorfen, flumiclorac, fomesafen, flumioxazin, sulfentrazone, bifenox, chlomethoxyfen, chlornitrofen, ethoxyfen, fluorodifen, fluoroglycofen, fluoronitrofen, furyloxyfen, halosafen, nitrofen, nitrofluorfen, oxyfluorfen, fluazolate, pyraflufen, cinidon-ethyl, flumipropyn, fluthiacet, thidiazimin, oxadiazon, oxadiargyl, azafenidin, carfentrazone, pentoxazone, benzfendizone, butafenacil, pyraclonil, profluazol, flufenpyr, flupropacil, nipyraclofen and etnipromid, as well as other herbicides discussed herein, including 3-phenyluracils of Formula I given herein above. Recombinant plants, recombinant plant cells, recombinant plant tissue and recombinant herbicide resistant plants include those which have been engineered to delete a glycine (or functionally equivalent) residue from the PPO protein at a position homologous to Gly210 or Gly211 of SEQ ID NO:16, but which do not contain heterologous DNA sequences (thus being nontransgenic in that sense).

Also provided by the present disclosure are methods for rendering a plant of interest resistant to PPO-inhibiting herbicides. A method of the present invention comprises the steps of introducing a vector comprising a DNA construct containing a constitutive transcriptional regulatory sequence (active in a plant) operably linked to a coding sequence for an herbicide resistant PPO of the present invention into a plant cell or tissue to produce a transgenic plant cell or transgenic plant tissue which is resistant to PPO-inhibiting herbicides including, but not limited to, lactofen, acifluorfen, flumiclorac, fomesafen, flumioxazin, bifenox, chlomethoxyfen, chlornitrofen, ethoxyfen, fluorodifen, sulfentrazone, fluoroglycofen, fluoronitrofen, furyloxyfen, halosafen, lactofen, nitrofen, nitrofluorfen, oxyfluorfen, fluazolate, pyraflufen, cinidon-ethyl, flumipropyn, fluthiacet, thidiazimin, oxadiazon, oxadiargyl, azafenidin, carfentrazone, sulfentrazone, pentoxazone, benzfendizone, butafenacil, pyraclonil, profluazol, flufenpyr, flupropacil, nipyraclofen and etnipromid and to the herbicidal 3-phenyluracils disclosed herein above.

In addition to introducing a coding sequence of an herbicide resistant PPO, the present invention provides for genetically modifying a plant cell or plant tissue so to delete one codon of a glycine-glycine codon pair in the coding sequence of an herbicide sensitive PPO or of one of an alanine pair or of one residue of an alanine-glycine or glycine-alanine pair in the region homologous to the glycine pair at amino acids 210-211 of SEQ ID NO:16, the waterhemp wildtype sequence, which is converted to a single glycine or functionally equivalent amino acid residue in the specifically exemplified mutant PPO of the present invention), thereby converting that coding sequence to one of an herbicide resistant PPO, as taught herein, and then regenerating a plant from that genetically modified cell or tissue. This strategy has the advantage that the genetically modified plant does not retain any exogenous nucleic acid sequences and thus, poses no danger with respect to dissemination of drug resistance traits or carrying any known allergenic proteins derived from a heterologous plant. This is advantageously accomplished using a recombinagenic oligonucleotide lacking the noted codon.

Also, the present disclosure provides methods for selecting or screening for a genetic modification event, for example transformation, via the expression of the PPO-inhibiting herbicide resistant coding sequence of the present invention after introduction into a cell or tissue of interest the coding sequence operably linked to transcription control sequences functional in that cell or tissue. Similarly, one can select for a genetically engineered herbicide resistance mutation as taught herein or one can select for the presence of a gene comprising an introduced mutation (introduced via a recombinagenic, mutagenic oligonucleotide, for example).

The present invention further encompasses transgenic and engineered plants expressing an herbicide resistant PPX2L coding sequence as disclosed herein. For the specifically exemplified coding sequences, see SEQ ID NOs 13, 25, 29 and 45. Specifically exemplified herbicide-resistant PPO enzymes of the present invention include those of SEQ ID NOs: 14, 26 and 30. Alternatively, a PPO coding sequence of a plant of interest can be modified so as to delete a glycine (or alanine or functionally equivalent) residue at a position homologous to that encoding Gly210 or Gly 211 of SEQ ID NO:16 so that the PPO protein corresponds to the specifically exemplified herbicide resistant PPO, i.e., having the PPO enzyme activity but insensitive to the aforementioned herbicides. Such a plant can be engineered by art known techniques to alter the native sequence so as to delete the codon for a glycine residue as taught herein.

Also within the scope of the present disclosure are cultivated Amaranthus species (including, but not limited to, A. hypochondriacus, A. cruentus, A. caudatus, A. dubius, and A. tricolor) into which the herbicide resistant PPO gene from the weed A. tuberculatus has been introduced by conventional plant breeding and selection techniques. Other crops of interest into which a herbicide resistant PPO gene of the present invention can be introduced or engineered (without the incorporation of heterologous DNA sequence information as discussed herein) include, without limitation, cotton, corn, wheat, rice, oats, barley, vegetables including crucifers (cabbage, Brussels sprouts, kale, kohl rabi, broccoli and the like), tomatoes, potatoes, sunflowers, peppers, eggplants, stone fruits, berries, grapes, apples, pears, tobacco, petunias and ornamental plants including roses, shrubs, turf and grasses.

Additional embodiments relate to transformed seeds and transgenic progeny plants of the parent transgenic or otherwise genetically modified plant of the invention and the use of said plants, seeds, and plant parts in the agro-industry and/or in the production of food, feed, industrial products, oil, nutrients, and other valuable products. Preferably, these other embodiment of the invention relates to transformed seed of such a plant, method for breeding other plants using said plant, use of said plant in breeding or agriculture, and use of said plant to produce chemicals, food or feed products. Similarly, seeds, plants and progeny plants into which the glycine (or a functionally equivalent) deletion which confers the relevant herbicide resistance phenotype has been engineered are also embodiments of the present invention.

The present invention further provides a method for identifying a target site for introducing a deletion mutation to create an herbicide resistance gene in a plant of interest. First, a search against a plant protein database for PPO sequences is carried out using a sequence such as (but not limited to) amino acids 201-218 of SEQ ID NO:16, 18, 20, 22 or 28, as the query sequence and requiring at least a match of about 75%, in this case 14 out of 18 amino acids. Alternatively, amino acids 195-220 of SEQ ID NO:16, 18, 20, 22 or 28 could be used as the query sequence, with 75% match. Inspection of the subject related sequence allows identification of a glycine or an alanine (or other functionally equivalent amino acid) residue within said subject sequence, and then a recombinagenic oligonucleotide is designed using the coding sequence for the subject sequence, with the sequence of the recombinagenic oligonucleotide lacking an alanine or glycine or other codon of interest. Reference is made to Table 20, in which a number of subject sequences are set forth and the underlined alanine and glycine residues represent those for which deletion of one such residue results in the herbicide resistance phenotype. Then, a recombinagenic oligonucleotide lacking the relevant codon is introduced into cells of the cognate plant cell, the phenotype selected and a plant regenerated. Appropriate selection and breeding procedures produce a plant which is homozygous for the herbicide resistance trait. Progeny plants and seeds as well as plant cells and plant tissue with the resistance deletion mutation are also within the scope of this invention.

Also provided by the present disclosure are methods for controlling the growth of unwanted plants amongst crop or other plants containing and expressing a PPO-inhibiting herbicide resistant PPX2L coding sequence of the present invention or a functionally equivalent engineered herbicide resistant PPO, where the crop or other plants are cultivated and sprayed with a PPO-inhibiting herbicide, with the result that the unwanted plants, which are naturally sensitive to a PPO-inhibiting herbicide, are killed or retarded in growth. Thus, the crop or other plants of interest grow with greater efficiency and with less competition for nutrients, sunlight and water from unwanted species.

A further aspect of the present invention is an assay to determine the presence of the waterhemp Gly210 deletion mutation, using the PCR assay and primers described herein below. Ascertaining the prevalence of this mutation in a weed population allows the agriculturist or horticulturist to formulate an efficient and economical weed control strategy. Where this deletion mutation is prevalent, then an herbicide other than a PPO-inhibiting herbicide is advantageously chosen for weed control.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows Lactofen responses of the protoporphyrinogen oxidase inhibitor-susceptible parent (S), -resistant parent (R), hybrid where the maternal parent was R {F₁(R)}, or hybrid where the maternal parent was S {F₁(S)}. Waterhemp plants were harvested 15 days after treatment with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) Crop Oil Concentrate (COC). Boxes represent the 25^(th) to 75^(th) percentile of responses, while whiskers include the remaining quartiles (n=100).

FIG. 2 provides the Lactofen dose-response curves of the protoporphyrinogen oxidase inhibitor-susceptible parent (S=♦), -resistant parent (R=◯), hybrid where the maternal parent was R {F₁(R)=Δ}, or hybrid where the maternal parent was S {F₁(S)=▴}. Waterhemp plants were harvest 15 days after treatment. Vertical bars represent +/− the standard error of the mean (n=12).

FIGS. 3A-3B show protoporphyrinogen oxidase inhibitor dose-response curves of the susceptible parent (S=♦), resistant parent (R=◯), hybrid where the maternal parent was R {F₁(R)=Δ}, or hybrid where the maternal parent was S {F₁(S)=▴} with two PPO-inhibiting herbicides. Waterhemp plants were harvested 10 days after treatment. Vertical bars represent +/− the standard error of the mean (n=12).

FIG. 4 shows the results of PCR-based molecular marker analysis of PPX1 or PPX2L alleles. A. tuberculatus plants used in the study were derived from F₁ hybrids backcrossed to the S parent (BC_(S)). Markers were used to determine if the F₁-derived pollen carried the S or R parental allele. BC_(S) plants were treated with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) COC and harvested 15 days after treatment. Vertical bars represent +/− the standard error of the mean (PPX1, n=42 or 40 for S or R parental alleles, respectively; PPX2L, n=39 or 49 for S or R parental alleles, respectively)

FIG. 5 shows selected amino acid residues of N. tabacum PPO2 in proximity to the herbicide-binding site. A. tuberculatus plants resistant to PPO inhibitors are missing a glycine residue equivalent to G178 of N. tabacum. This amino acid deletion is predicted to hinder PPO inhibitor binding. Letter abbreviations are: amino acid residues, D=aspartic acid, G=glycine, C=cysteine, T=threonine; PPO-inhibiting herbicide, Flz=fluazolate.

FIG. 6 illustrates PPO expression in a hemG mutant strain of E. coli. E. coli cells were grown on LB medium alone or supplemented with hematin (20 μg ml⁻¹) or lactofen (100 nM). E. coli isolates were: C1 and C2, non-transformed controls; S1 and S2, transformed with vector encoding A. tuberculatus-derived PPO2L with glycine at position 210; R1 and R2, transformed with vector encoding identical PPO2L with the exception of a deletion of glycine at position 210.

FIG. 7 provides translated PPX2L amino acid sequences from A. tuberculatus. Amino acid differences are indicated by “*”. Amino acid position 210 (black boxes) is the only difference that correlates with R or S responses to lactofen (GenBank accessions DQ386114, DQ386117, DQ386116, and DQ386118 and SEQ ID NO:22, 28, 26 and 30, respectively).

FIG. 8 shows partial coding regions of the 5′ end of PPX2L from A. tuberculatus. The three-bp deletion leading to a G210 deletion in PPX2L from R plants was identified within the ninth exon starting from the 5′ end (see also SEQ ID NO:43 and 44 for the sequences from the sensitive and resistant genes, respectively).

FIG. 9 shows the results of Southern blot analysis of A. tuberculatus genomic DNA probed with a fragment of PPX2L. DNA was isolated from plants that were derived from the R or S biotype and digested with EcoRI or HindIII.

FIGS. 10A-10B provide a summary of positions within the A. tuberculatus PPX2L coding sequence which can be varied without either loss of function and without affecting herbicide resistance. In FIG. 10A the reference sequence is SEQ ID NO:15 (herbicide sensitive PPX2L), and in FIG. 10B, SEQ ID NO:13 (herbicide resistant PPX2L) Such varied sequences represent polymorphisms.

DETAILED DESCRIPTION OF THE INVENTION

Despite being used to control weeds in agricultural crops for the past 30 years, the mode-of-action of herbicides inhibiting protoporphyrinogen oxidase (PPO) was mostly unknown for the first 20 years of their use. Multiple chemical structures inhibit PPO, with the diphenylethers, triazolinones, and N-phenyl-phthalimides being the major families used in crop production.

PPO is the last common enzyme in the tetrapyrrole biosynthetic pathway that produces heme and chlorophyll (Beale and Weinstein 1990). In plants, chlorophyll biosynthesis takes place exclusively in chloroplasts, while heme is produced in both plastids and mitochondria (Smith et al. 1993; Chow et al. 1997). The tetrapyrrole biosynthetic pathway in plants begins with the formation of 5-aminolevulinic acid (ALA) from the C5-skeleton of glutamate. Eight molecules of ALA are combined to form protoporphyrinogen IX (protogen IX) (Papenbrock and Grimm 2001). Protogen IX is converted to protoporphyrin IX (proto IX) in both chloroplasts and mitochondria by the activity of PPO (Jacobs and Jacobs 1984). Studies conducted by Matringe et al. (1992) provided evidence that two constitutive PPO activities are found in chloroplasts: one associated with envelope membranes and another with thylakoid membranes. In mitochondria, PPO is associated exclusively with the envelope membranes (Deybach et al. 1985).

The genes that encode either plastid PPO (PPX1) or mitochondrial PPO (PPX2) have recently been cloned and sequenced from several plant species (Lermontova et al. 1997; Watanabe et al. 2001). Both PPX1 and PPX2 are nuclear encoded genes whose translation products must be imported into plastids or mitochondria, respectively. Interestingly, the translated product of PPX2 from spinach has been identified in two isoforms of different length due to the existence of dual in-frame initiation codons (Watanabe et al. 2001). The longer version of PPX2 includes a sequence encoding a chloroplast transit peptide, while the shorter version encodes a targeting sequence for import into the mitochondria.

When susceptible plants are treated with PPO inhibitors, the substrate of PPO, protogen IX, accumulates and is exported from the plastid to the cytoplasm (Kojima et al. 1991; Jacobs and Jacobs 1993) where herbicidally insensitive peroxidase-like enzymes in the plasma membrane convert it to proto IX (Lee et al. 1993; Lee and Duke 1994; Retzlaff and Böger 1996). Proto IX accumulates in the cytoplasm, and in the presence of light, induces the formation of singlet oxygen (Cox and Whitten 1983) that is damaging to cell membranes. Symptomatology following PPO inhibitor treatment occurs rapidly in the presence of light, with water soaked lesions and tissue necrosis appearing within hours after treatment (Dayan and Duke 1997).

Plants or plant cells resistant to PPO inhibitors have been generated by tissue culture selection (Horikoshi and Hirooka 1999; Pornprom et al. 1994; Wantanabe et al. 1998) and genetic engineering (Choi et al. 1998; Lee et al. 2000; Lermontova and Grimm 2000). Acifluorfen-resistant mutants of Arabidopsis thaliana have also been reported (Duke et al. 1997); however, no characterization related to resistance has been reported. Considerable effort has been devoted to the development of PPO inhibitor-resistant crops (Reviewed by Li and Nicholl 2005), but none are believed to have been commercialized.

PPO inhibitor resistance in waterhemp was first documented in Kansas during the summer of 2000 (Shoup et al. 2003). In Illinois, a waterhemp biotype resistant to PPO inhibitors was first identified during the summer of 2001 (Patzoldt et al. 2005). According to Dayan and Duke (1997), resistance to PPO-inhibiting herbicides can be achieved by one of six predicted methods: 1) reduced herbicide uptake, 2) enhanced herbicide metabolism before reaching its site of action, 3) altered herbicide site of action, 4) removal or degradation of protogen 1× from the cytoplasm before it can be converted to proto IX, 5) inactivated extraplastidic PPO-like enzymes, and 6) sequestration of singlet oxygen and other toxic species. Other mechanisms of PPO inhibitor resistance might also be: 7) over-expression of the plastid form of PPO (Lermontova and Grimm 2000) and 8) over-expression of the mitochondrial form of PPO (Watanabe et al. 1998). Numerous structurally diverse compounds inhibit PPO, indicating that this herbicide target site is highly variable, similar to the target sites of herbicides that inhibit ALS or acetyl-CoA carboxylase (ACCase) (Duke et al. 1997). Currently, at least 18 amino acid substitutions have been identified within PPO that confer resistance to PPO-inhibiting herbicides (Volrath et al. 1999).

Waterhemp is the first weed species to have been selected for resistance to PPO inhibitors; thus it provides a unique opportunity for characterization of herbicide resistance mechanisms in plants. Therefore, the objectives of this study related to PPO inhibitor resistance were determine the inheritance, calculate the degree of dominance, and determine the mechanism of resistance in waterhemp.

As used herein, an herbicide resistant plant is one which germinates from a seed and/or grows in the concentration of pesticide where the comparison wild-type plant does not grow and/or does not germinate. The germination and growth of the resistant plant is similar in the presence or absence of the relevant PPO-inhibiting herbicide.

For recombinant production of the enzyme in a host organism, the PPO coding sequence is inserted into an expression cassette designed for the chosen host and introduced into the host where it is recombinantly produced. The choice of specific regulatory sequences such as promoter, signal sequence, 5′ and 3′ untranslated sequences, and enhancer, is within the level of skill of the one ordinarily skilled in the art. The resultant molecule, containing the individual elements linked in proper orientation and reading frame, may be inserted into a vector capable of being transformed into the host cell. Suitable expression vectors and methods for recombinant production of proteins are well known for host organisms such as E. coli (see, e.g. Studier and Moffatt. 1986. J. Mol. Biol. 189: 113; Brosius. 1989. DNA 8: 759), yeast (see, e.g., Schneider and Guarente. 1991. Meth. Enzymol. 194: 373) and insect cells (see, e.g. Luckow and Summers. 1988. Bio/Technol. 6: 47). Specific examples include plasmids such as pBluescript (Stratagene, La Jolla, Calif.), pFLAG (International Biotechnologies, Inc., New Haven, Conn.), pTrcHis (Invitrogen, Carlsbad, Calif.), and baculovirus expression vectors, e.g., those derived from the genome of Autographica california nuclear polyhedrosis virus (AcNPV). A preferred baculovirus/insect system is pV111392/Sf21 cells (Invitrogen, Carlsbad, Calif.).

A recombinantly produced herbicide resistant PPO of the present invention is useful for a variety of purposes, including, but not limited to, in an in vitro assay to screen known herbicidal compounds to determine if they inhibit this PPO, in an in vitro general screening assay to identify chemicals which do or do not inhibit the mutant PPO, or to characterize its association with known inhibitors in order to rationally design new inhibitory herbicides as well as herbicide tolerant forms of the enzyme.

The inhibitory effect on PPO can be determined by measuring fluorescence at about 622 to 635 nm, after excitation at about 395 to 410 nM (see, e.g. Jacobs and Jacobs. 1982. Enzyme 28: 206; Sherman et al. 1991. Plant Physiol. 97, 280). Protoporphyrin IX is a fluorescent pigment; protoporphyrinogen IX is not fluorescent. Protein extracts are prepared from selected subcellular fractions, e.g. etioplasts, mitochondria, microsomes, or plasma membrane, by differential centrifugation (see, e.g. Lee et al. 1993. Plant Physiol. 102:881; Prado et al. 1979. Plant Physiol. 65: 956; Jackson and Moore, in Plant Organelles, Reid, ed., pp. 1-12; Jacobs and Jacobs. 1993. Plant Physiol. 101: 1181). Protoporphyrinogen is prepared by reduction of protoporphyrin with a sodium amalgam as described by Jacobs and Jacobs (1982). Reactions mixtures typically consist of 100 mM Hepes (pH 7.5), 5 mM EDTA, 2 mM DTT, about 2 μM protoporphyrinogen IX, and about 1 mg/mL protein extract. Inhibitor solutions in various concentrations, e.g. 1 mM, 100 μM, 10 μM, 1 μM, 100 nM, 10 nM, 1 nM, 100 pM, are added to the enzyme extract prior to the initiation of the enzyme reaction. Once the protein extract is added, fluorescence is monitored for several minutes, and the slope of the slope (reaction rate) is calculated from a region of linearity. IC₅₀ is determined by comparing the slope of the inhibited reaction to a control reaction, and IC₅₀ is the concentration of herbicide at which the reaction rate of the wild type enzyme is reduced by 50%.

Herbicides that inhibit wild type PPO enzymes include many different structural classes of molecules (Duke et al. 9119. Weed Sci. 39: 465; Nandihalli et al. 1992. Pesticide Biochem. Physiol. 43: 193; Matringe et al. 1989. FEBS Lett. 245: 35; Yanase and Andoh. 1989. Pesticide Biochem. Physiol. 35: 70), including the diphenylethers (e.g. acifluorifen, 5-{2-chloro-4-(trifluoromethyl)phenoxy}-2-nitrobezoic acid; its methyl ester; or oxyfluorfen, 2-chloro-1-(3-ethoxy-4-nitrophenoxy)-4-(trifluorobenzene)), oxidiazoles (e.g. oxidiazon, 3-{2,4-dichloro-5-(1-methylethoxy)phenyl}-5-(1,1-dimethylethyl)-1,3,4-oxadiazol-2-(3H)-one), cyclic imides (e.g. S-23142, N-(4-chloro-2-fluoro-5-propargyloxyphenyl)-3,4,5,6-tetrahydrophthalimide; chlorophthalim, N-(4-chlorophenyl)-3,4,5,6-tetrahydrophthalimide), phenyl pyrazoles (e.g. TNPP-ethyl, ethyl 2-{1-(2,3,4-trichlorophenyl)-4-nitropyrazolyl-5-oxy}propionate; M&B 39279), pyridine derivatives (e.g. LS 82-556), and phenopylate and its O-phenylpyrrolidino- and piperidinocarbamate analogs. The herbicidal activity of the above compounds is described in the Proceedings of the 1991 Brighton Crop Protection Conference, Weeds (British Crop Protection Council), Proceedings of the 1993 Brighton Crop Protection Conference, Weeds (British Crop Protection Council), U.S. Pat. Nos. 4,746,352 and 1993 Abstracts of the Weed Science Society of America vol. 33, pg. 9.

The imide herbicides include those classified as aryluracils and having the general formula wherein R signifies the group (C₂₋₆-alkenyloxy)carbonyl-C₁₋₄-alkyl, as disclosed in U.S. Pat. No. 5,183,492. See also WO 94/08999, WO 93/10100, and U.S. Pat. No. 5,405,829 assigned to Schering; N-phenylpyrazoles, 3-substituted-2-aryl-4,5,6,7-tetrahydroindazoles (Lyga et al. 1994. Pesticide Sci. 42:29-36).

Additional herbicides for which resistant crops and resistant ornamental plants are needed include those listed previously pertaining to the 3-phenyl uracils, such as those of Formula I as defined herein above.

Effective application rates of herbicide which normally are inhibitory to the activity of PPO are known in the art, for example, 0.0001 to 10 kg/ha, preferably from 0.005 to 2 kg/ha. Rates depend, at least in part, on external factors such as environment, time and method of application. This dosage rate or concentration of herbicide depends on the desired action and particular compound used, and can be determined by methods known in the art.

The present invention is further directed to transgenic plants, transgenic progeny plants, transgenic seeds, transgenic cells and transgenic plant tissue resistant to herbicides that inhibit the naturally occurring PPO activity in these plants, wherein the tolerance is conferred by an herbicide resistant PPO enzyme of the present invention. Plants, progeny plants, seeds, cells and tissue which are genetically engineered to delete a particular alanine or glycine (or functionally equivalent) codon of a PPO gene as taught herein with the result of herbicide resistance, are also within the scope of the present invention. Representative plants include any plants to which these herbicides are applied for their normally intended purpose, especially agronomically important angiosperms and gymnosperms, including but not limited to, cotton, soya, rape, sugar beet, maize, rice, wheat, barley, oats, rye, sorghum, millet, forage, turf grasses, berries, vegetables, stone fruits, grapevines, apples, pears, ornamental plants, tree species and the like.

The present invention also encompasses plants, progeny plants, seeds, plant tissue and plant cells which contain (and express) a genetically engineered PPO coding sequence for an herbicide resistant protein, with the coding sequence being characterized by the deletion of a glycine or alanine (or functionally equivalent) codon and where the herbicide resistance is dependent on the deletion of the glycine or alanine (or functionally equivalent) residue in the protein. The alanine or glycine residue (or functionally equivalent) which is targeted for deletion is identified in a sequence alignment of a PPO amino acid sequence of interest using amino acids 201-218 of one of SEQ ID NOs:16, 18, 20, 22 or 28, as specifically exemplified, with the alanine or glycine aligning with either amino acid 210 or 211 of one of SEQ ID NOs:16, 18, 20, 22 or 28. The relevant portion of the coding sequence for the targeted protein is found, especially in a sequence databank, and a recombinagenic oligonucleotide is designed and synthesized with deletion of the codon for the amino acid to be deleted in the resulting protein. Advantageously, the glycine or alanine (or functionally equivalent) codon of interest is deleted by homologous recombination of a mutagenic oligonucleotide, in which there is identity to the sequences flanking the codon in the genomic coding sequence, which is introduced into a plant cell of interest, for example by biolistic transformation or other means of introducing nucleic acid known to the art. The plant cell is incubated so as to allow recombination and expression of the mutated coding sequence, and then recombination events can be selected by placing the plant cell in contact with an herbicide-containing culture medium, thus selecting of those cells which contain and express the mutated sequence encoding the herbicide resistant PPO. Then the plant cells are regenerated to product herbicide resistant genetically engineered plants. Recombinagenic oligonucleotides and mutagenesis techniques using same are known to the art; see, e.g., U.S. Pat. Nos. 6,879,075; 5,565,350; US Patent Publications 2005/0044597; 2007/0028318; 2007/0033670; Beetham et al. (1999) Proc. Natl. Acad. Sci. US 96:8774-8778; Zhu et al. (1999) Proc. Natl. Acad. Sci. US 96:8768-8773; Zhu et al. (2000) Nature Biotech. 18:555-558; Kochevenko and Willmitzer (2003) Plant Physiol. 132:174-184; Okazuki and Toriyama (2004) Plant Cell Rep. 22:509-412; Dong et al. (2006) Plant Cell Rep. 25:457-465, for example. Recombinogenic oligonucleotide technology is described in U.S. Pat. No. 5,565,350, for example.

In the context of the present invention, an “herbicide resistant PPO” is a PPO activity different from that which occurs in a wild-type (herbicide-sensitive). Such a resistant PPO is one which is not inhibited significantly (more than 90%) by a “PPO-inhibiting” herbicide set forth herein.

Plants expressing the herbicide resistant PPO can be obtained by stably transforming an herbicide resistant PPO coding sequence of the present invention into a plant cell such that it is expressed in the above-ground plant tissues, and preferably in all plant tissues, and it stably maintained in the plant. Herbicide resistant PPO coding sequences can be obtained or identified by complementing a bacterial or yeast auxotrophic mutant with a cDNA expression library from the target plant. Alternatively, an herbicide sensitive PPX2L coding sequence can be converted to encode the resistant phenotype by site-directed mutagenesis to delete one of the two contiguous glycine codons for amino acid residues 210-211 of SEQ ID NO:16, 18, 20, 22 or 28 or a functional equivalent thereof.

The herbicide resistant PPO sequence of the present invention was obtained by cloning a PPO gene from a plant that was naturally resistant to PPO-inhibiting herbicides including lactofen, acifluorfen, flumiclorac, fomesafen, flumioxazin, and sulfentrazone. Specifically, a population of waterhemp was identified that was no longer effectively controlled by PPO-inhibiting herbicides.

An alternative strategy for producing an herbicide resistant plant cell, herbicide resistant plant tissue or an herbicide resistant plant is the introduction of a DNA molecule with a nucleotide sequence engineered to be identical with the native PPO coding sequence except that one of two glycine codons, two alanine codons or an alanine or Glycine codon of an alanine-glycine or a glycine-alanine (or functionally equivalent) pair corresponding to positions 210-211 of the specifically exemplified PPO coding sequence of A. tuberculatus as set forth in SEQ ID NOs:15, 17, 19, 21 or 27 is deleted. See Table 19 for alignments to show how the corresponding positions are identified (underlined in subject sequences). Alternatively, one of an alanine pair or one of an alanine-glycine or one of a glycine-alanine (or functionally equivalent) pair aligning with amino acids 210-211 of SEQ ID NO:16, 18, 20, 22 or 28 can be deleted to produce an herbicide resistant PPO. Selection for the resistance phenotype recovers those plant cells in which homologous recombination has resulted in deletion of one of the two contiguous glycine or functionally equivalent residues in the native gene. Regeneration of a plant results in an engineered plant which does not contain any heterologous genetic information but which does express an herbicide resistant PPO protein; thus allowing growth of the plant in the presence of herbicide. The absence of heterologous genetic information can facilitate regulatory approval of the plant, reduce the likelihood of deleterious health effects in consumers and provide for greater acceptance of the use of the plants in agriculture or the environment that occurs with those transgenic plants into which foreign nucleic acid sequences have been introduced. The technology for this type of genetic engineering is well known to the art. See, e.g., U.S. Pat. Nos. 5,565,350, 6,870,075; US Published Applications 2007/0033670, 2007/0028318, 2005/0044597, 2005/0177899; Beetham et al. Proc. NAtl. Acad, Sci. USA 96:8774-8778, Kochevenko and Lillmitzer (2003) Plant Physiol. 132:174-184, Zhu et al. Proc. NAtl. Acad, Sci. USA 96:8768-8773, Zhu et al. (2000) Nature Biotechnol. 18:555-558, Okazaki and Toriyama (2000) Plant Cell Rep. 22:509-512, Dong et al. (2006) Plant Cell Rep. 25:457-465, among others.

Recombinagenic oligonucleobases (also termed recombinagenic oligonucleotides herein) and their use to effect genetic changes in eukaryotic cells are described in U.S. Pat. No. 5,565,350 to Kmiec. The '350 patent teaches a method for introducing specific genetic alterations into a target gene. It discloses recombinagenic oligonucleobases having two strands, in which a first strand contains two segments of at least 8 RNA-like nucleotides that are separated by a third segment of from 4 to about 50 DNA-like nucleotides, termed an “interposed DNA segment.” The nucleotides of the first strand are base paired to DNA-like nucleotides of a second strand. The first and second strands are additionally linked by a segment of single stranded nucleotides so that the first and second strands are parts of a single oligonucleotide chain. The '350 patent further teaches a method for introducing specific genetic alterations into a target gene. According to the '350 patent, the sequences of the RNA segments are selected to be homologous, i.e., identical, to the sequence of a first and a second fragment of the target gene. The sequence of the interposed DNA segment is homologous with the sequence of the target gene between the first and second fragment except for a region of difference, termed the “heterologous region.” The heterologous region can effect an insertion or deletion, or can contain one or more bases that are mismatched with the sequence of target gene so as to effect a substitution. According to the '350 patent, the sequence of the target gene is altered as directed by the heterologous region, such that the target gene becomes homologous with the sequence of the recombinagenic oligonucleotide. The '350 patent specifically teaches that ribose and 2′-O-methylribose, i.e., 2′-methoxyribose, containing nucleotides can be used in recombinagenic oligonucleotides and that naturally-occurring deoxyribose-containing nucleotides can be used as DNA-like nucleotides.

U.S. Pat. No. 5,731,181 to Kmiec specifically disclose the use of recombinagenic oligonucleobases to effect genetic changes in plant cells and discloses further examples of analogs and derivatives of RNA-like and DNA-like nucleotides that can be used to effect genetic changes in specific target genes. Other patents discussing the use of recombinagenic oligonucleobases include: U.S. Pat. Nos. 5,756,325; 5,871,984; 5,760,012; 5,888,983; 5,795,972; 5,780,296; 5,945,339; 6,004,804; and 6,010,907 and in International Patent No. PCT/US00/23457; and in International Patent Publications WO 98/49350; WO 99/07865; WO 99/58723; WO 99/58702; and WO 99/40789.

Recombinagenic oligonucleotides include mixed duplex oligonucleotides, non-nucleotide containing molecules taught in U.S. Pat. No. 5,731,181 and other molecules taught in the above-noted patents and patent publications.

The recombinagenic oligonucleotide can be introduced into a plant cell using any method commonly used in the art, including but not limited to, microcarriers (biolistic delivery), microfibers, electroporation, and microinjection. An oligonucleobase is a polymer of nucleobases, which polymer can hybridize by Watson-Crick base pairing to a DNA having the complementary sequence, i.e., the target sequence into which the mutation is to be introduced.

Nucleobases comprise a base, which is a purine, pyrimidine, or a derivative or analog thereof (i.e., they may be modified nucleotides or nucleotides). Nucleobases include peptide nucleobases, the subunits of peptide nucleic acids, and morpholine nucleobases as well as nucleosides and nucleotides. Nucleosides are nucleobases that contain a pentosefuranosyl moiety, e.g., an optionally substituted riboside or 2′-deoxyriboside. Nucleosides can be linked by one of several linkage moieties, which may or may not contain phosphorus. Nucleosides that are linked by unsubstituted phosphodiester linkages are termed nucleotides. Alternative linkages may provide at least some resistance to degradation by the nucleases in the cells into which the oligonucleotides or oligonucleobases are introduced.

An oligonucleobase chain has a single 5′ and 3′ terminus, which are the ultimate nucleobases of the polymer. A particular oligonucleobase chain can contain nucleobases of all types. An oligonucleobase compound is a compound comprising one or more oligonucleobase chains that are complementary and hybridized by Watson-Crick base pairing. Nucleobases are either deoxyribo-type or ribo-type. Ribo-type nucleobases are pentosefuranosyl containing nucleobases wherein the 2′ carbon is a methylene substituted with a hydroxyl, alkyloxy or halogen. Deoxyribo-type nucleobases are nucleobases other than ribo-type nucleobases and include all nucleobases that do not contain a pentosefuranosyl moiety.

An oligonucleobase strand generically includes both oligonucleobase chains and segments or regions of oligonucleobase chains. An oligonucleobase strand has a 3′ end and a 5′ end. When an oligonucleobase strand is coextensive with a chain, the 3′ and 5′ ends of the strand are also 3′ and 5′ termini of the chain.

The invention is also directed to the culture and regeneration of cells mutated according to the methods of the present invention in order to obtain a plant that produces seeds, henceforth a “fertile plant”, and the production of seeds and additional plants from such a fertile plant, with those plants exhibiting the herbicide resistance phenotype as described herein.

Examples of constitutive promoters which function in plant cells include the cauliflower mosaic virus (CaMV) 19S or 35S promoters, CaMV 35S double or enhanced promoters, the 35S promoter and an enhanced or double 35S promoter such as that described in Kay et al., Science 236: 1299-1302 (1987); nopaline synthase promoter; pathogenesis-related (PR) protein promoters, the rice actin promoter (McElroy et al. 1991. Mol. Gen. Genet. 231: 150), maize ubiquitin promoter (EP 0 342 926; Taylor et al. 1993. Plant Cell Rep. 12: 491), and the Pr-1 promoter from tobacco, Arabidopsis, or maize (see U.S. Pat. No. 5,614,395), the peanut chlorotic streak caulimovirus (PCISV) promoter (U.S. Pat. No. 5,850,019), the 35S promoter from cauliflower mosaic virus (CaMV) (Odell et al. 1985. Nature 313:810-812), promoters of Chlorella virus methyltransferase genes (U.S. Pat. No. 5,563,328), the full-length transcript promoter from figwort mosaic virus (FMV) (U.S. Pat. No. 5,378,619); the promoters from such genes as rice actin (McElroy et al. 1990. Plant Cell 2:163-171), ubiquitin (Christensen et al. 1989. Plant Mol. Biol. 12:619-632) and Christensen et al. 1992. Plant Mol. Biol. 18:675-689), pEMU (Last et al. 1991. Theor. Appl. Genet. 81:581-588), MAS (Velten et al. 1984. EMBO J. 3:2723-2730), maize H3 histone (Lepetit et al. 1992. Mol. Gen. Genet. 231:276-285 and Atanassova et al. 1992. Plant Journal 2(3):291-300), Brassica napus ALS3 (WO 97/41228); and promoters of various Agrobacterium genes (see, e.g., U.S. Pat. Nos. 4,771,002, 5,102,796, 5,182,200 and 5,428,147). Light-regulated promoters suitable for expression in above-ground tissues include the small subunit of ribulose bisphosphate carboxylase (ssuRUBISCO) promoter and the like. The promoters themselves may be modified to manipulate promoter strength to increase herbicide resistant PPO expression, in accordance with art-recognized procedures.

Guidance for the design of promoters is provided by studies of promoter structure, such as that of Harley and Reynolds. 1987. Nucleic Acids Res. 15:2343-2361). Also, the location of the promoter relative to the transcription start may be optimized. See, e.g., Roberts, et al. 1979. Proc. Natl. Acad. Sci. USA 76:760-4. Many suitable promoters for use in plants are well known in the art.

Suitable inducible promoters for use in plants include: the promoter from the ACE1 system which responds to copper (Mett et al. 1993. PNAS 90:4567-4571); the promoter of the maize ln2 gene which responds to benzenesulfonamide herbicide safeners (Hershey et al. 1991. Mol. Gen. Genetics 227:229-237) and Gatz et al. 1994. Mol. Gen. Genetics 243:32-38), and the promoter of the Tet repressor gene from Tn10 (Gatz et al. 1991. Mol. Gen. Genet. 227:229-237). A particularly preferred inducible promoter for use in plants is one that responds to an inducing agent to which plants do not normally respond. An exemplary inducible promoter of this type is the inducible promoter from a steroid hormone gene, the transcriptional activity of which is induced by a glucocorticosteroid hormone (Schena et al. 1991. Proc. Natl. Acad. Sci. USA 88:10421) or the recent application of a chimeric transcription activator, XVE, for use in an estrogen receptor-based inducible plant expression system activated by estradiol (Zuo et al. 2000. The Plant Journal 24:265-273). Other inducible promoters for use in plants are described in, e.g., EP 332104, WO 93/21334 and WO 97/06269. Plant promoters composed of portions of other promoters and partially or totally synthetic promoters can also be used; see, e.g., Ni et al. 1995. Plant J. 7:661-676; WO 95/14098.

The promoter may include or be modified to include one or more enhancer elements. Promoters with enhancer elements provide for higher levels of transcription as compared to promoters without them. Suitable enhancer elements for use in plants include the PCISV enhancer element (U.S. Pat. No. 5,850,019), the CaMV 35S enhancer element (U.S. Pat. Nos. 5,106,739 and 5,164,316) and the FMV enhancer element (Maiti et al. 1997. Transgenic Res. 6:143-156). See also WO 96/23898 and Enhancers and Eukaryotic Expression (Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 1983).

A 5′ untranslated sequence is also employed. The 5′ untranslated sequence is the portion of an mRNA which extends from the 5′ CAP site to the translation initiation codon. This region of the mRNA is necessary for translation initiation in plants and plays a role in the regulation of gene expression. Suitable 5′ untranslated regions for use in plants include those of alfalfa mosaic virus, cucumber mosaic virus coat protein gene, and tobacco mosaic virus.

For efficient expression, the coding sequences are preferably also operatively linked to a 3′ untranslated sequence. The 3′ untranslated sequence will include a transcription termination sequence and a polyadenylation sequence. The 3′ untranslated region can be obtained from the flanking regions of genes from Agrobacterium, plant viruses, plants or other eukaryotes. Suitable 3′ untranslated sequences for use in plants include those of the cauliflower mosaic virus 35S gene, the phaseolin seed storage protein gene, the pea ribulose biphosphate carboxylase small subunit E9 gene, the soybean 7S storage protein genes, the octopine synthase gene, and the nopaline synthase gene.

The PPO gene of the present invention advantageously contains both chloroplast and mitochondrial transit peptides. Others known to the art can be substituted, if deemed advantageous.

The chimeric DNA construct(s) (non-naturally occurring nucleic acid molecules) of the invention may contain multiple copies of a promoter or multiple copies of the herbicide resistant PPO coding sequence of the present invention. In addition, the construct(s) may include coding sequences for selectable or detectable markers, each in proper reading frame with the other functional elements in the DNA molecule. The preparation of such constructs is within the ordinary level of skill in the art.

The DNA construct may be a vector. The vector may contain one or more replication systems which allow it to replicate in host cells. Self-replicating vectors include plasmids, cosmids and viral vectors. Alternatively, the vector may be an integrating vector which allows the integration into the host cell's chromosome of the DNA sequence encoding the herbicide resistant PPO. The vector desirably also has unique restriction sites for the insertion of DNA sequences. If a vector does not have unique restriction sites, it may be modified to introduce or eliminate restriction sites to make it more suitable for further manipulations.

The DNA constructs of the invention can be used to transform any type of plant cells (see below). A genetic marker must be used for selecting transformed plant cells (a selection marker). Selection markers typically allow transformed cells to be recovered by negative selection (i.e., inhibiting growth of cells that do not contain the selection marker) or by screening for a product encoded by the selection marker.

The most commonly used selectable marker gene for plant transformation is the neomycin phosphotransferase II (nptII) gene, isolated from Tn5, which, when placed under the control of plant expression control signals, confers resistance to kanamycin (Fraley et al. 1983. Proc. Natl. Acad. Sci. USA 80:4803). Another commonly used selectable marker gene is the hygromycin phosphotransferase gene which confers resistance to the antibiotic hygromycin. Vanden Elzen et al. 1995. Plant Mol. Biol. 5:299). Additional selectable marker genes of bacterial origin that confer resistance to antibiotics include gentamicin acetyl transferase, streptomycin phosphotransferase, aminoglycoside-3′-adenyl transferase, and the bleomycin resistance determinant (Hayford et al. 1988. Plant Physiol. 86:1216; Jones et al. 1987. Mol. Gen. Genet. 210:86; Svab et al. 1990. Plant Mol. Biol. 14:197; HiIle et al. 1986. Plant Mol. Biol. 7:171). Other selectable marker genes confer resistance to herbicides such as glyphosate, glufosinate or bromoxynil (Comai et al. 1985. Nature 317:741-744; Stalker et al. 1988. Science 242:419-423; Hinchee et al. 1988. Bio/Technology 6:915-922; Stalker et al. 1988. J. Biol. Chem. 263:6310-6314; Gordon-Kamm et al. 1990. Plant Cell 2:603-618).

Other selectable markers useful for plant transformation include, without limitation, mouse dihydrofolate reductase, plant 5-enolpyruvylshikimate-3-phosphate synthase, and plant acetolactate synthase (Eichholtz et al. 1987. Somatic Cell Mol. Genet. 13:67; Shah et al. 1986. Science 233:478; Charest et al. 1990. Plant Cell Rep. 8:643; EP 154,204), and herbicide resistance markers including, or other than, the PPO derivatives of the present invention.

Commonly used genes for screening presumptively transformed cells include but are not limited to β-glucuronidase (GUS), β-galactosidase, luciferase, and chloramphenicol acetyltransferase (Jefferson, R. A. 1987. Plant Mol. Biol. Rep. 5:387; Teeri et al. 1989. EMBO J. 8:343; Koncz et al. 1987. Proc. Natl. Acad. Sci. USA 84:131; De Block et al. 1984. EMBO J. 3:1681), green fluorescent protein (GFP) (Chalfie et al. 1994. Science 263:802; Haseloff et al. 1995. TIG 11:328-329 and PCT application WO 97/41228). Another approach to the identification of relatively rare transformation events has been use of a gene that encodes a dominant constitutive regulator of the Zea mays anthocyanin pigmentation pathway (Ludwig et al. 1990. Science 247:449).

The level of resistance of a particular resistant PPO can be tested using transgenic plant cells, transgenic plant tissue (such as callus, for example) or transgenic plant. Resistance can also be confirmed using direct selection in plants. For example, the effect of an herbicide such those as described above, on the growth inhibition of plants such as wild-type Arabidopsis, soybean, or maize may be determined by plating seeds sterilized by art-recognized methods on plates on a simple minimal salts medium containing increasing concentrations of the inhibitor. Such concentrations are in the range of 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30, 110, 300, 1000 and 3000 parts per million (ppm). The lowest dose at which significant growth inhibition can be reproducibly detected is used for subsequent experiments with transgenic plants, cells, etc. Alternatively, heme auxotrophic E. coli expressing the PPO can be used in testing.

Two approaches can be taken to confirm that the genetic basis of the resistance of a transgenic plant is a PPO of the present invention. First, alleles of the PPO gene from plants exhibiting resistance to the inhibitor can be isolated using PCR with primers based either upon the mutant region(s) in the resistant cDNA sequence shown in SEQ ID NO:13, or a functionally equivalent sequence. The herbicide resistant enzyme of the present invention can be expressed in a plant of interest after incorporation into a pCambia vector under the transcriptional control of the CaMV 35S promoter, the Arabidopsis actin-2 promoter or the native waterhemp PPO promoter, among others well known in the art). Many gene expression systems for plants are well known and readily accessible to the art.

To characterize the resistance mechanism in wild waterhemp, plants from a PPO inhibitor-resistant (R) A. tuberculatus biotype were reciprocally crossed with wild type (herbicide-susceptible, S) plants to create F₁ lines, followed by subsequent crossing to generate F₂ and backcross (BC) lines. In response to the PPO inhibitor, lactofen, the resultant A. tuberculatus lines segregated for resistance in ratios similar to those expected for a single genetic unit of inheritance (Table 1). Furthermore, plants from lines that were homozygous or heterozygous for resistance survived 53-fold or 31-fold higher doses of lactofen, respectively, when compared with S plants (FIG. 2; Table 2). Thus, resistance to lactofen was inherited as a single, incompletely dominant gene.

F₂ lines derived from the same male (half-sib lines) were not significantly different; therefore, the data from lines were combined. Results of F₂ progenies treated with lactofen segregated as expected if resistance were inherited as a single gene, with a segregation of 3:1 (R:S) (Table 1). Similarly, BC_(S) or BC_(R) lines responded as expected, with a 1:1 or 1:0 segregation for R:S lactofen responses, respectively (Table 1). Because there was no difference in lactofen resistance when it was inherited from the maternal or paternal parent, resistance to lactofen is assumed to be nuclear encoded. The results of these experiments suggest that PPO inhibitor resistance in the R waterhemp biotype is inherited as a single, nuclear encoded gene.

Herbicide dose-response experiments were conducted on the S parent, R parent, or F₁ lines to determine the dominance of PPO inhibitor resistance using the methods of Stone (1968) based on the calculation of GR₅₀ values. When waterhemp plants were harvested 15 days after lactofen treatment, dominance values of 0.72 or 0.76 were estimated using F₁(R) or F₁(S) lines, respectively (where 0 to 1=dominant, 0=partially dominant, or 0 to −1=recessive) (Table 2, FIG. 2). However, a potential problem with these results was that waterhemp plants might have been past their linear phase of growth, thus leading to an overestimate of dominance. Therefore, waterhemp plants used in subsequent dose-response experiments were harvested 10 DAT, and were challenged with lactofen or acifluorfen. Dominance values of −0.06 or 0.56 were estimated using F₁(R) or F₁(S) lines, respectively, in response to lactofen 10 DAT (Table 2, FIG. 3). In response to acifluorfen calculated 10 DAT, dominance values of 0.34 or 0.46 were estimated using F₁(R) or F₁(S) lines, respectively (Table 2, FIGS. 3A-3B). Results from all dominance experiments suggest that PPO inhibitor resistance in the R biotype is incompletely dominant because nearly all estimated dominance values ranged between 0 and 1.

To carry out molecular characterization of PPX genes from waterhemp, complementary DNA (cDNA) sequences that encode PPO isozymes were obtained from R and S A. tuberculatus plants, but with unexpected results. From S plants, cDNA sequences for PPX1, PPX2, and a longer version of PPX2, PPX2L, were identified and amino acid sequences encoded were deduced; See SEQ ID NOs: 17-18, 19-20 and 21-22; GenBank Accession Nos. DQ386112, DQ386113, and DQ386114. It is noted that PPO1, PPO2 and PPO2L refer to the proteins encoded by the genes PPX1, PPX2 (shorter sequence also termed PPX2S) and PPX2L, respectively. In this application where PPO is recited, it is synonymous with PPX2L unless otherwise obvious from context. Comparison of translated sequences of PPX2 and PPX2L indicated that they shared 98% amino acid identity, with the exception of a 30 amino acid extension in the 5′ end that was unique to PPX2L. This extension is predicted to encode a signaling sequence for plastid import (Emmanuelson, 2000). Thus, it was thought that the PPX2L gene isolated from A. tuberculatus likely encodes both plastid- and mitochondria-targeted PPO isoforms due to the presence of alternate in-frame initiation codons, a phenomenon that was reported previously for Spinacia oleracea (spinach) PPX2 (Watanabe, 2001). In comparison, PPX1 shared 26% and 25% amino acid identity with PPX2 and PPX2L, respectively, and thus is an evolutionarily distinct isozyme. From R plants, only PPX1 and PPX2L genes (See SEQ ID NOs:23-24 and 25-26; GenBank Accession Nos. DQ386115 and DQ386116, respectively) were identified based on cDNA sequencing. To confirm the lack of PPX2 identification in R plants, Southern blot analysis was performed using genomic DNA probed with a fragment of PPX2L. Probing with the fragment of PPX2L identified two major bands (presumably PPX2 and PPX2L loci) from S plants, but only a single major band (presumably the PPX2L locus) from R plants, thus confirming the results obtained from sequencing efforts (FIG. 9). Without wishing to be bound by theory, it is believed that the PPX1 from the lactofen resistant waterhemp does not contribute to the resistant phenotype, and that the two different lengths of PPX2 resulted from two alleles of the PPX2 locus.

To determine whether PPX1 or PPX2L mediated PPO inhibitor resistance, polymerase chain reaction (PCR)-based molecular markers were used to follow the inheritance of alleles of these two genes in A. tuberculatus lines segregating 1:1 for R or S responses to lactofen. The molecular marker for PPX2L was significantly correlated with lactofen responses (P<0.0001), while the marker for PPX1 was not (P=0.4278) (FIG. 4). In other words, plants were resistant to lactofen only if they inherited the PPX2L allele from the R parent. Results of molecular markers studies focused further efforts toward differences among PPX2L alleles.

Inspection of the amino acid sequences of PPX2L among S and R plants revealed two amino acid polymorphisms that were correlated with resistance. In an attempt to identify only a single amino acid polymorphism, additional R and S plants were sequenced from independently identified A. tuberculatus biotypes (See SEQ ID NOs:27-28 and 29-30; GenBank accessions DQ386117 and DQ386118). Sequencing results and subsequent comparisons identified three additional amino acid polymorphisms (five total); however, only one, a glycine deletion at position 210 (ΔG210), was consistently polymorphic between all R and S plants analyzed (FIG. 7). PPX2L also was sequenced using genomic DNA (gDNA) as a template (See SEQ ID NOs:31-32 and 33-34; GenBank Accession Nos. DQ394875 and DQ394876 for S and R plants, respectively) to further confirm the existence of the three-bp deletion corresponding to the G210 codon. Alignment of gDNA and cDNA sequences of PPX2L identified the codon corresponding to the G210 residue in the ninth exon when starting from the 5′ end (FIG. 8). The three-bp deletion was also identified in PPX2L gDNA sequences of R plants, therefore indicating that the ΔG210 mutation in PPO2L was not the result of an error introduced during mRNA processing.

The relationship of PPX2S and PPX2L has been studied to determine whether they represented two genetic loci or alleles of a single locus. Segregation analysis was used to examine the relationship between PPX2S and PPX2L. A cleaved amplified polymorphic sequence (CAPS) marker was designed based on an SNP previously identified (Genbank Accession Nos. DQ386114, DQ386113) between these genes (Patzoldt et al. 2006). WCS (herbicide sensitive waterhemp population, Wayne County, IL) individuals were screened to identify plants containing both PPX2S and PPX2L markers. A single male and several females with this genotype were allowed to cross and seed was collected from individual females. Two of the resultant F1 populations were tested for segregation of the SNP marker with the following expectations: if PPX2S and PPX2L are distinct loci, every individual in the F1 population would be expected to have markers for both genes. Alternatively, if PPX2S and PPX2L represent alleles of the same locus, the alleles should segregate in the F1 population in a 1:2:1 ratio. The results of two crosses were consistent with the independent segregation of two alleles defining a single genetic locus.

Sequence analysis was used to further examine the alleles at the PPX2 locus. Using sequence from grain amaranth genomic DNA (gDNA), primers were designed to amplify a fragment containing the 5′ end of the PPX2 gene, including the transit peptide sequence. The sequence of this fragment from two WCS (Wayne County, IL, herbicide sensitive waterhemp population) individuals, one individual from the ACR (Adams County, IL, herbicide resistant waterhemp population), and one F1 individual from the cross that was previously determined to be homozygous for the PPX2S marker, were compared. In every case, two in-frame start codons were identified in this fragment. These data are consistent with a single PPX2 locus in waterhemp containing two translation initiation codons and thus encoding proteins that are predicted to be targeted to two different subcellular locations.

Previous studies suggested the presence of a short form of PPX2, PPX2S, which encoded a protein with only a mitochondrial targeting sequence similar to the PPX2 proteins described in mouse-ear cress (Arabidopsis thaliana L. Heynh.), soybean (Glycine max (L.) Merr.), and potato (Solanum tuberosum L.). This PPX2S sequence was only found in sensitive biotypes of waterhemp. This conclusion was based on both Southern blot and sequence data. However, the experiments described herein above led to the conclusion instead that waterhemp contains a single PPX2 locus. In light of these experiments and without wishing to be bound by any particular theory, the present inventors believe that the Southern blot data were most likely misleading due to heterozygosity at the PPX2L locus in the sensitive biotype while the resistant biotype was homozygous at this locus. With this in mind, a close examination of 5′-RACE sequence data from previous experiments revealed that the PPX2S sequence in fact included nearly the entire 5′ end of the PPX2L gene. Therefore, again without wishing to be bound by theory, the inventors believe that PPX2L most likely represents the only PPX2 gene in waterhemp; i.e., waterhemp does not contain a “PPX2S”. This is a phenomenon that previously has been seen in both spinach (Spinach oleracea) and corn (Zea mays) (Watanabe et al. 2001). With regards to herbicide-resistance evolution, it remains to be determined if a herbicide-resistant PPX2 gene must contain dual-targeting sequences to provide resistance at the whole plant level. If this characteristic promotes resistance, it is believed that weeds containing a PPX2L gene would evolve resistance to PPO-inhibitors faster than those lacking a dual-targeted PPX2.

The ΔG210 allele of PPX2L is unique; it is the first instance for which a deletion mutation has been shown to be the mechanism of resistance to any herbicide. To examine the prevalence of this mutation in waterhemp populations resistant to PPO-inhibitors, an allele-specific PCR marker was designed to amplify the ΔG210 allele of PPX2L. First, to test the accuracy of this assay, the marker was used to follow the inheritance of the ΔG210 allele of PPX2L in an F2 population from an ACR×WCS cross where the deletion mutation was previously shown to be sufficient to confer herbicide resistance. Individuals from this population were scored for the presence of the PCR marker then treated with lactofen to identify herbicide-resistant individuals. As expected, the presence of the marker was highly correlated with herbicide resistance (P<1e-12). Next, to test the prevalence of the deletion mutation in other known resistant populations, six plants each from four populations were tested with the PCR marker then treated with a single application of lactofen. The marker was highly correlated with herbicide resistance in all of these populations as well.

While the selection of such a unique sequence would be expected to be rare, these data suggest this allele is the predominant mechanism of resistance and, in fact, the only mechanism of resistance thus far identified among waterhemp populations in Illinois. The contribution of gene flow to the dispersal of this sequence was not considered in this study. However, there are polymorphisms between the resistant allele of PPX2L from ACR and that of a resistant biotype from Clinton County (CCR) (Genbank Accession Nos. DQ386118, DQ386116) suggesting that the ΔG210 allele of PPX2L was independently selected as the resistance mechanism in multiple waterhemp populations. This could indicate that the ΔG210 allele represents the mutation that confers the highest level of resistance while maintaining the lowest fitness penalty for single mutation in the gene. Alternatively, perhaps waterhemp is more prone to insertion/deletion polymorphisms than SNPs and, thus, there is a better chance that resistance mechanisms are based on indel polymorphisms. As described by Patzoldt et al. (2006) and Gressel and Levy (2006), the repeat nature of the nucleotide sequence within and proximal to the G210 codon in waterhemp PPX2L may foster indel mutations.

The ΔG210 mutation was also assessed using the resolved protein structure of PPO2 from Nicotiana tabacum (tobacco) as a reference (Koch, 2004; Martz, 2002). The equivalent amino acid to G210 of A. tuberculatus PPO2L (G178 of N. tabacum PPO) was located near the herbicide-binding site, thus supporting the prediction that the G210 deletion was responsible for herbicide resistance (FIG. 5). It is understood that a G211 deletion is equivalent in function to the G210 deletion mutant enzymes described herein, and either a G210 or a G211 deletion can be combined with any of the polymorphisms set forth in FIGS. 10A-10B.

The ΔG210 mutation appears to be the predominant resistance mechanism in waterhemp. This is significant because it is both economically and environmentally beneficial to be able to identify herbicide-resistant weeds before the application of a herbicide. Oftentimes such identification requires lengthy and/or labor-intensive bioassays because, in the case of many herbicides, multiple mechanisms exist by which plants can exhibit resistance. Herein we have described a PCR-based assay that accurately predicts resistance to the PPO-inhibiting herbicides in all six resistant populations tested. This simple yet robust assay is a valuable tool for weed management decisions. In an effort to characterize the sensitivity of this assay for field use, leaf samples of resistant and sensitive waterhemp were pooled to simulate sampling a field. Pools were created by progressively diluting the resistant leaf sample with sensitive leaf samples. Genomic DNA was isolated from these pools and then used as template in PCR. The presence of ΔG210 was reliably detected in pools where the resistant leaf sample represented 25% of the total sample. With additional modifications well understood and readily accessible to the art (e.g., quantitative real-time PCR), this assay could be made more sensitive and quantitative. From a practical standpoint, however, the use of a PPO-inhibiting herbicide could be recommended, at least as a rescue treatment, if less than 25% of the weed population (and all or most of the crop or ornamental plant population) were resistant.

The exemplary sequences of the waterhemp sensitive and resistant PPO proteins are given in SEQ ID NOs:16, 18, 20, 22 and 28 and NOs:14, 24, 26 and 30, respectively. CAA73866 (Nicotiana tabacum, SEQ ID NO:55), BAA76348 (Glycine max, SEQ ID NO:56), BAB08301 (A. thaliana, SEQ ID NO:57), CAA73865 (tobacco, SEQ ID NO:58), AAV97809 (A. thaliana, SEQ ID NO:59), AAF00194 (chickory, SEQ ID NO:60) and the consensus sequence are in aligned in Table 19, together with representative of the aforementioned waterhemp sequences. Table 20 shows the aligned with the relevant A. tuberculatus sequence encompassing amino acids 201-218 of SEQ ID NO:16.

A search of certain protein databases was undertaken, using amino acids 201 to 218 of SEQ ID NO:16 (herbicide sensitive PPO waterhemp) as the query sequence against the 780,949 sequences available on the internet on available sequence databases, including genbankpln0.aa; gbrefplant0.aa protein databases, and the BLAST 2.2.12 program. Searching and alignment was carried out essentially as described in Altschul et al. (1997), “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs”, Nucleic Acids Res. 25:3389-3402. Perfect match and alignments were found for wildtype waterhemp sequences, which are disclosed herein and for which the details are not shown below. Additional sequences from database PPO proteins were found, with the corresponding sequences being shown below. Those 18 amino acid sequences from sensitive and resistant PPO proteins which were disclosed in the present application have not been included in the detailed information given below.

TABLE 19 Alignment of PPO Sequences waterhemp_sensi --------------------------------- MVIQSITHLSPNLALPSPLSVSTKNYP waterhemp_resis --------------------------------- MVIQSITHLSPNLALPSPLSVSTKNYP CAA73866 ------------------------------------------------------------ BAA76348 ------------------------------------------------------------ BAB08301 --------------MGLIKNGTLYCRFGISWNFAAVFFSTYFRHCFRLVRDFDSELLQIA CAA73865 -MTTTPIANHPNIFTHQSSSSPLAFLNRTSFIPFSSISKRNS-VNCNG-WRTRCSVAKDY AAV97809 --------------------MELSLLRPTTQSLLPSFSKPNLRLNVYKPLRLRCSVAGGP AAF00194 MTSLTDVCSLNCCRSWSSLPPPVSGGSLTSKNPRYLITYSPAHRKCNR-WRFRCSIAKDS consensus ----------------------l------s-----i-s-t----n---------sl---- waterhemp_sensi VAVMGNISEREEPTSAKRVAVVGAGVSGLAAAYKLKSHG---- LSVTLFEADSRAGGKLK waterhemp_resis VAVMGNISEREEPTSAKRVAVVGAGVSGLAAAYKLKSHG---- LSVTLFEADSRAGGKLK CAA73866 ---MAPSAGEDKHSSAKRVAVIGAGVSGLAAAYKLKIHG----LNVTVFEAEGKAGGKLR BAA76348 ---MASSATDDNPRSVKRVAVVGAGVSGLAAAYKLKSHG----LDVTVFEAEGRAGGRLR BAB08301 MASGAVADHQIEAVSGKRVAVVGAGVSGLAAAYKLKSRG----LNVTVFEADGRVGGKLR CAA73865 TVPSSAVDGG--PAAELDCVIVGAGISGLCIAQVMSANYP----NLMVTEARDRAGGNIT AAV97809 TVGSSKIEGGGGTTITTDCVIVGGGISGLCIAQALATKHPDAAPNLIVTEAKDRVGGNII AAF00194 PITPP-ISNEFNSQPLLDCVIVGAGISGLCIAQALATKHASVSPDVIVTEARDRVGGNIS consensus ---mg-i---e-ptsakrvavvGaGvSGLaaAyklkshg----lnvtvfEAd-raGGklk waterhemp_sensi TVKKDGFIWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNP waterhemp_resis TVKKDGFIWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNP CAA73866 SVSQDGLIWDEGANTMTESEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSNP BAA76348 SVSQDGLIWDEGANTMTESEIEVKGLIDALGLQEKQQFPISQHKRYIVKNGAPLLVPTNP BAB08301 SVMQNGLIWDEGANTMTEAEPEVGSLLDDLGLREKQQFPISQKKRYIVRNGVPVMLPTNP CAA73865 TVERDGYLWEEGPNSFQPSDP-MLTMAVDCGLKDDLVLGDPNAPRFVLWKGKLRPVPSKL AAV97809 TREENGFLWEEGPNSFQPSDP-MLTMVVDSGLKDDLVLGDPTAPRFVLWNGKLRPVPSKL AAF00194 TVERDGYLWEEGPNSFQPSDA-MLTMVVDSGLKDDLVLGDPTAPRFVLWGGDLKPVPSKP consensus tv-kdGfiWdEGaNtmteseaev-sliddlGLrekqqlpisq-kRyivrnG-pvllPsnp waterhemp_sensi AALLTSNILSAKSKLQIMLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDP waterhemp_resis AALLTSNILSAKSKLQIMLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDP CAA73866 IDLIKSNFLSTGSKLQMLLEPILWKNKKLSQVSDSH--ESVSGFFQRHFGKEVVDYLIDP BAA76348 AALLKSKLLSAQSKIHLIFEPFMWKRSDPSNVCDENSVESVGRFFERHFGKEVVDYLIDP BAB08301 IELVTSSVLSTQSKFQILLEPFLWKKKS-SKVSDASAEESVSEFFQRHFGQEVVDYLIDP CAA73865 TDLAFFDLMSIPGKLRAGFGAIGLRP------SPPGHEESVEQFVRRNLGGEVFERLIEP AAV97809 TDLPFFDLMSIGGKIRAGFGALGIRP------SPPGREESVEEFVRRNLGDEVFERLIEP AAF00194 ADLPFFDLMSFPGKLRAGFGALGFRP------SPPDREESVEEFVRRNLGDEVFERLIEP consensus adLl-s-llS--sKlqim-epflwrk---t-lsd---eESV-eFf-RhfGkEvvdylIdP waterhemp_sensi FVAGTCGGDPQSLSMHHTFPEVWNIEKRFGSVFAGLIQSTLLSKKEK-- GGENASIKKPR waterhemp_resis FVAGTCG-DPQSLSMHHTFPEVWNIEKRFGSVFAGLIQSTLLSKKEK-- GGENASIKKPR CAA73866 FVAGTCGGDPDSLSMHHSFPELWNLEKRFGSVILGAIRSKLSPKNEKKQGPPKTSANKKR BAA76348 FVGGTSAADPESLSMRHSFPELWNLEKRFGSIIAGALQSKLFAKREKTGENRTALRKNKH BAB08301 FVGGTSAADPDSLSMKHSFPDLWN---SFGSIIVGAIRTKFAAKGGKSRDTKSSPGTKKG CAA73865 FCSGVYAGDPSKLSMKAAFGKVWKLEETGGSIIGGTFKAIK-ERSSTPKAPRDPRLPKPK AAV97809 FCSGVYAGDPSKLSMKAAFGKVWKLEQNGGSIIGGTFKAIQ-ERKNAPKAERDPRLPKPQ AAF00194 FCSGVYAGDPSKLSMKAAFGKVWNLEQNGGSIVGGAFKAIQ-DRKNSQKPPRDPRLPKPK consensus FvaGt-agDP-sLSMkhtFpevWnlekrfGSiiaGairs-l--kkek-rg-r---i-kpr waterhemp_sensi VRGSFSFQGGMQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWSVSSMSNN--T waterhemp_resis VRGSFSFQGGMQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWSVSSMSNN--T CAA73866 QRGSFSFLGGMQTLTDAICKDLREDELRLNSRVLELSCSCTEDSAIDSWSIISASPHKRQ BAA76348 KRGSFSFQGGMQTLTDTLCKELGKDDLKLNEKVLTLAYGHDGSSSSQNWSITSASNQ--- BAB08301 SRGSFSFKGGMQILPDTLCKSLSHDEINLDSKVLSLSYNSG--SRQENWSLSCVSHN--- CAA73865 GQTVGSFRKGLRMLPDAISARLG-SKLKLSWKLSSITK-----SEKGGYHLTYETPEG-- AAV97809 GQTVGSFRKGLRMLPEAISARLG-SKVKLSWKLSGITK-----LESGGYNLTYETPDG-- AAF00194 GQTVGSFRKGQAMLPNAISTRLG-SRVKLCWKLTSISK-----LENRGYNLTYETPQG-- consensus -rgsfSFkgGmqtLpd-ick-Lg-delkLq-kvlslsy-----s--gnwslts-spn--- waterhemp_sensi SEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEVTYVPLSVMITAFKKDKVKRP-- waterhemp_resis SEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEVTYVPLSVMITAFKKDKVKRP-- CAA73866 SEEESFDAVIMTAPLCDVKSMKIAKRGNPFLLNFIPEVDYVPLSVVITTFKRENVKYP-- BAA76348 -STQDVDAVIMTAPLYNVKDIKITKRGTPFPLNFLPEVSYVPISVMITTFKKENVKRP-- BAB08301 -ETQRQNPHYDAAPLCNVKEMKVMKGGQPFQLNFLPEINYMPLSVLITTFTKEKVKRP-- CAA73865 --VVSLQSRSIVMTVPSYVASNILRPLSVAAADALSNFYYPPVGAVTITYPQEAIRDERL AAV97809 --LVSVQSKSVVMTVPSHVASGLLRPLSESAANALSKLYYPPVAAVSISYPKEAIRTECL AAF00194 --FESLQTKTIVMTVPSYVASDLLRPLSLGAADALSKFYYPPVAAVSISYPKDAIRADRL consensus -e-qsvdavvvtapi-nvkemkimk-g-pf-l-flpev-YvPlsvvittfkke-vkrp-- waterhemp_sensi --------------------------------- MVIQSITHLSPNLALPSPLSVSTKNYP waterhemp_resis --------------------------------- MVIQSITHLSPNLALPSPLSVSTKNYP CAA73866 ------------------------------------------------------------ BAA76348 ------------------------------------------------------------ BAB08301 --------------MGLIKNGTLYCRFGISWNFAAVFFSTYFRHCFRLVRDFDSELLQIA CAA73865 -MTTTPIANHPNIFTHQSSSSPLAFLNRTSFIPFSSISKRNS-VNCNG-WRTRCSVAKDY AAV97809 --------------------MELSLLRPTTQSLLPSFSKPNLRLNVYKPLRLRCSVAGGP AAF00194 MTSLTDVCSLNCCRSWSSLPPPVSGGSLTSKNPRYLITYSPAHRKCNR-WRFRCSIAKDS consensus ----------------------l------s-----i-s-t----n---------sl---- waterhemp_sensi VAVMGNISEREEPTSAKRVAVVGAGVSGLAAAYKLKSHG---- LSVTLFEADSRAGGKLK waterhemp_resis VAVMGNISEREEPTSAKRVAVVGAGVSGLAAAYKLKSHG---- LSVTLFEADSRAGGKLK CAA73866 ---MAPSAGEDKHSSAKRVAVIGAGVSGLAAAYKLKIHG----LNVTVFEAEGKAGGKLR BAA76348 ---MASSATDDNPRSVKRVAVVGAGVSGLAAAYKLKSHG----LDVTVFEAEGRAGGRLR BAB08301 MASGAVADHQIEAVSGKRVAVVGAGVSGLAAAYKLKSRG----LNVTVFEADGRVGGKLR CAA73865 TVPSSAVDGG--PAAELDCVIVGAGISGLCIAQVMSANYP----NLMVTEARDRAGGNIT AAV97809 TVGSSKIEGGGGTTITTDCVIVGGGISGLCIAQALATKHPDAAPNLIVTEAKDRVGGNII AAF00194 PITPP-ISNEFNSQPLLDCVIVGAGISGLCIAQALATKHASVSPDVIVTEARDRVGGNIS consensus ---mg-i---e-ptsakrvavvGaGvSGLaaAyklkshg----lnvtvfEAd-raGGklk waterhemp_sensi TVKKDGFIWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNP waterhemp_resis TVKKDGFIWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNP CAA73866 SVSQDGLIWDEGANTMTESEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSNP BAA76348 SVSQDGLIWDEGANTMTESEIEVKGLIDALGLQEKQQFPISQHKRYIVKNGAPLLVPTNP BAB08301 SVMQNGLIWDEGANTMTEAEPEVGSLLDDLGLREKQQFPISQKKRYIVRNGVPVMLPTNP CAA73865 TVERDGYLWEEGPNSFQPSDP-MLTMAVDCGLKDDLVLGDPNAPRFVLWKGKLRPVPSKL AAV97809 TREENGFLWEEGPNSFQPSDP-MLTMVVDSGLKDDLVLGDPTAPRFVLWNGKLRPVPSKL AAF00194 TVERDGYLWEEGPNSFQPSDA-MLTMVVDSGLKDDLVLGDPTAPRFVLWGGDLKPVPSKP consensus tv-kdGfiWdEGaNtmteseaev-sliddlGLrekqqlpisq-kRyivrnG-pvllPsnp waterhemp_sensi AALLTSNILSAKSKLQIMLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDP waterhemp_resis AALLTSNILSAKSKLQIMLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDP CAA73866 IDLIKSNFLSTGSKLQMLLEPILWKNKKLSQVSDSH--ESVSGFFQRHFGKEVVDYLIDP BAA76348 AALLKSKLLSAQSKIHLIFEPFMWKRSDPSNVCDENSVESVGRFFERHFGKEVVDYLIDP BAB08301 IELVTSSVLSTQSKFQILLEPFLWKKKS-SKVSDASAEESVSEFFQRHFGQEVVDYLIDP CAA73865 TDLAFFDLMSIPGKLRAGFGAIGLRP------SPPGHEESVEQFVRRNLGGEVFERLIEP AAV97809 TDLPFFDLMSIGGKIRAGFGALGIRP------SPPGREESVEEFVRRNLGDEVFERLIEP AAF00194 ADLPFFDLMSFPGKLRAGFGALGFRP------SPPDREESVEEFVRRNLGDEVFERLIEP consensus adLl-s-llS--sKlqim-epflwrk---t-lsd---eESV-eFf-RhfGkEvvdylIdP waterhemp_sensi FVAGTCGGDPQSLSMHHTFPEVWNIEKRFGSVFAGLIQSTLLSKKEK-- GGENASIKKPR waterhemp_resis FVAGTCG-DPQSLSMHHTFPEVWNIEKRFGSVFAGLIQSTLLSKKEK-- GGENASIKKPR CAA73866 FVAGTCGGDPDSLSMHHSFPELWNLEKRFGSVILGAIRSKLSPKNEKKQGPPKTSANKKR BAA76348 FVGGTSAADPESLSMRHSFPELWNLEKRFGSIIAGALQSKLFAKREKTGENRTALRKNKH BAB08301 FVGGTSAADPDSLSMKHSFPDLWN---SFGSIIVGAIRTKFAAKGGKSRDTKSSPGTKKG CAA73865 FCSGVYAGDPSKLSMKAAFGKVWKLEETGGSIIGGTFKAIK-ERSSTPKAPRDPRLPKPK AAV97809 FCSGVYAGDPSKLSMKAAFGKVWKLEQNGGSIIGGTFKAIQ-ERKNAPKAERDPRLPKPQ AAF00194 FCSGVYAGDPSKLSMKAAFGKVWNLEQNGGSIVGGAFKAIQ-DRKNSQKPPRDPRLPKPK consensus FvaGt-agDP-sLSMkhtFpevWnlekrfGSiiaGairs-l--kkek-rg-r---i-kpr waterhemp_sensi VRGSFSFQGGMQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWSVSSMSNN--T waterhemp_resis VRGSFSFQGGMQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWSVSSMSNN--T CAA73866 QRGSFSFLGGMQTLTDAICKDLREDELRLNSRVLELSCSCTEDSAIDSWSIISASPHKRQ BAA76348 KRGSFSFQGGMQTLTDTLCKELGKDDLKLNEKVLTLAYGHDGSSSSQNWSITSASNQ--- BAB08301 SRGSFSFKGGMQILPDTLCKSLSHDEINLDSKVLSLSYNSG--SRQENWSLSCVSHN--- CAA73865 GQTVGSFRKGLRMLPDAISARLG-SKLKLSWKLSSITK-----SEKGGYHLTYETPEG-- AAV97809 GQTVGSFRKGLRMLPEAISARLG-SKVKLSWKLSGITK-----LESGGYNLTYETPDG-- AAF00194 GQTVGSFRKGQAMLPNAISTRLG-SRVKLCWKLTSISK-----LENRGYNLTYETPQG-- consensus -rgsfSFkgGmqtLpd-ick-Lg-delkLq-kvlslsy-----s--gnwslts-spn--- waterhemp_sensi SEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEVTYVPLSVMITAFKKDKVKRP-- waterhemp_resis SEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEVTYVPLSVMITAFKKDKVKRP-- CAA73866 SEEESFDAVIMTAPLCDVKSMKIAKRGNPFLLNFIPEVDYVPLSVVITTFKRENVKYP-- BAA76348 -STQDVDAVIMTAPLYNVKDIKITKRGTPFPLNFLPEVSYVPISVMITTFKKENVKRP-- BAB08301 -ETQRQNPHYDAAPLCNVKEMKVMKGGQPFQLNFLPEINYMPLSVLITTFTKEKVKRP-- CAA73865 --VVSLQSRSIVMTVPSYVASNILRPLSVAAADALSNFYYPPVGAVTITYPQEAIRDERL AAV97809 --LVSVQSKSVVMTVPSHVASGLLRPLSESAANALSKLYYPPVAAVSISYPKEAIRTECL AAF00194 --FESLQTKTIVMTVPSYVASDLLRPLSLGAADALSKFYYPPVAAVSISYPKDAIRADRL consensus -e-qsvdavvvtapi-nvkemkimk-g-pf-l-flpev-YvPlsvvittfkke-vkrp--

TABLE 20 Sequences producing significant alignments included the following (bits) Value GBPLN: 88862005_88862006 mitochondrial PPO . . . 42 9e−04 GBPLN: 88809984_88809985 waterhemp mitochondrial PPO 42 9e−04 GBPLN: 88809978_88809979 waterhemp mitochondrial PPO 42 9e−04 GBPLN: 88809976_88809977 waterhemp 42 9e−04 GBPLN: 154269385_154269386 mitochondrial PPO 41 0.003 GBPLN: 2370334_2370335 PPO Nicotiana tabacum 40 0.003 GBPLN: 7544063_3093412 PPO Solanum tuberosum 40 0.003 GBPLN: 4105187_4105188 PPO PX-2 [Nicotiana . . . 40 0.003 GBPLN: 3929919_3929920 mitochondrial PPO 40 0.003 GBPLN: 14349152_14349153 PPO Spinacia 39 0.013 GBPLN: 147788410_147788412 protein Vitis vinifera 37 0.028 GBPLN: 32483304_38347440 Oryza sativa genomic DNA, chromosome 4, . . . 36 0.083 GBPLN: 32480009_38345232 Oryza sativa genomic DNA, chromosome 4, . . . 36 0.083 GBPLN: 88862007_88862008 mitochondrial PPO 35 0.11 GBPLN: 88809986_88809987 mitochondrial PPO 0.11 GBPLN: 88809982_88809983 mitochondrialPPO 35 0.11 GBREFPLANT: 162462665_162462666 PPO 33 0.54 GBPLN: 9857978_9857979 PPO (Zea mays) 33 0.54 GBPLN: 4586307_4586308 PPO Glycine max . . . 31 2.0 GBREFPLANT: 145358007_22326801 HEMG2/MEE61 (maternal effect embry . . . 30 3.5 GBREFPLANT: 30698605_22326801 HEMG2/MEE61 (maternal effect embryo . . . 30 3.5 GBPLN: 20856026_20856027 AT5g14220/MUA22_22 Arabidopsis thaliana 30 3.5 GBPLN: 18700120_18700121 AT5g14220/MUA22_22 Arabidopsis thaliana 30 3.5 GBPLN: 7573446_7573447 protoporphyrinogen oxidase-like protein A . . . 30 3.5 GBPLN: 2564050_9757803 protoporphyrinogen IX oxidase Arabidopsis . . . 30 3.5 In all cases in this table, the Query sequence was amino acids 201-218 of SEQ ID NO: 16. >GBPLN: 154269385_154269386 mitochondrial protoporphyrinogen oxidase (Amaranthus hypochondriacus) ABS72165.1 (EU024569) Length = 535 Score = 40.8 bits (94), Expect = 0.003 Identities = 17/18 (94%), Positives = 18/18 (100%) Query: 1 IDPFVAGTCGGDPQSLSM IDPFVAGTCGGDPQSLS+ Sbjct: 201 IDPFVAGTC GG DPQSLSV 218 (SEQ ID NO: 61) >GBPLN: 2370334_2370335 protoporphyrinogen oxidase (Nicotiana tabacum) CAA73866.1 (Y13466) Length = 504 Score = 40.4 bits (93), Expect = 0.003 Identities = 17/18 (94%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGTCGGDP SLSM Sbjct: 169 IDPFVAGTC GG DPDSLSM 186 (SEQ ID NO: 62) >GBPLN: 7544063_3093412 protoporphyrinogen oxidase (Solanum tuberosum) CAA12401.1 (AJ225108) Length = 404 Score = 40.4 bits (93), Expect = 0.003 Identities = 17/18 (94%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGTCGGDP SLSM Sbjct: 169 IDPFVAGTC GG DPDSLSM 186 (SEQ ID NO: 63) >GBPLN: 4105187_4105188 protoporphyrinogen oxidase PX-2 (Nicotiana tabacum) AAD02291.1 (AF044129) Length = 504 Score = 40.4 bits (93), Expect = 0.003 Identities = 17/18 (94%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGTCGGDP SLSM Sbjct: 169 IDPFVAGTC GG DPDSLSM 186 (SEQ ID NO: 64) >GBPLN: 3929919_3929920 mitochondrial protoporphyrinogen oxidase (Nicotiana tabacum) BAA34712.1 (AB020500) Length = 504 Score = 40.4 bits (93), Expect = 0.003 Identities = 17/18 (94%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGTCGGDP SLSM Sbjct: 169 IDPFVAGTC GG DPDSLSM 186 (SEQ ID NO: 65) >GBPLN: 14349152_14349153 protoporphyrinogen oxidase-II (Spinacia Oleracea) BAB60710.1 (AB046993) Length = 531 Score = 38.5 bits (88), Expect = 0.013 Identities = 17/18 (94%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGT GGDPQSLSM Sbjct: 200 IDPFVAGTS GG DPQSLSM 217 (SEQ ID NO: 66) >GBPLN: 147788410_147788412 hypothetical protein (Vitis vinifera) CAN69962.1 (AM453176) Length = 809 Score = 37.4 bits (85), Expect = 0.028 Identities = 16/18 (88%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGT GGDP+SLSM Sbjct: 185 IDPFVAGTS GG DPESLSM 202 (SEQ ID NO: 67) >GBPLN: 32483304_38347440 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0076N16, complete sequence. CAE02483.2 (AL731617) Length = 506 Score = 35.8 bits (81), Expect = 0.083 Identities = 15/18 (83%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGT GGDP+SLS+ Sbjct: 170 IDPFVAGTS GG DPESLSI 187 (SEQ ID NO: 68) >GBPLN: 32480009_38345232 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0084K20, complete sequence. CAE01661.2 (AL606613) Length = 506 Score = 35.8 bits (81), Expect = 0.083 Identities = 15/18 (83%), Positives = 17/18 (94%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFVAGT GGDP+SLS+ Sbjct: 170 IDPFVAGTS GG DPESLSI 187 (SEQ ID NO: 69) >GBREFPLANT: 162462665_162462666 protoporphyrinogen IX oxidase (Zea mays) NP_001105004.1 (NM_001111534) Length = 544 Score = 33.1 bits (74), Expect = 0.54 Identities = 13/18 (72%), Positives = 16/18 (88%) Query: 1 IDPFVAGTCGGDPQSLSM 18 +DPFVAGT  GDP+SLS+ Sbjct: 206 VDPFVAGTS AG DPESLSI 223 (SEQ ID NO: 70) >GBPLN: 9857978_9857979 protoporphyrinogen IX oxidase (Zea mays) AAG00946.1 (AF273767) Length = 544 Score = 33.1 bits (74), Expect = 0.54 Identities = 13/18 (72%), Positives = 16/18 (88%) Query: 1 IDPFVAGTCGGDPQSLSM 18 +DPFVAGT  GDP+SLS+ Sbjct: 206 VDPFVAGTS AG DPESLSI 223 (SEQ ID NO: 71) >GBPLN: 4586307_4586308 protoporphyrinogen IX oxidase (Glycine max) BAA76348.1 (AB025102) Length = 502 Score = 31.2 bits (69), Expect = 2.0 Identities = 13/18 (72%), Positives = 14/18 (77%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFV GT   DP+SLSM Sbjct: 171 IDPFVGGTS AA DPESLSM 188 (SEQ ID NO: 72) >GBREFPLANT: 145358007_22326801 HEMG2/MEE61 (maternal effect embryo arrest 61); (Arabidopsis thaliana) NP_196926.2 (NM_121426) Length = 508 Score = 30.4 bits (67), Expect = 3.5 Identities = 13/18 (72%), Positives = 13/18 (72%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFV GT   DP SLSM Sbjct: 173 IDPFVGGTS AA DPDSLSM 190 (SEQ ID NO: 73) >GBREFPLANT: 30698605_22326801 HEMG2/MEE61 (maternal effect embryo arrest 61); (Arabidopsis thaliana) NP_196926.2 (NC_003076) Length = 508 Score = 30.4 bits (67), Expect = 3.5 Identities = 13/18 (72%), Positives = 13/18 (72%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFV GT   DP SLSM Sbjct: 173 IDPFVGGTS AA DPDSLSM 190 (SEQ ID NO: 74) >GBPLN: 20856026_20856027 AT5g14220/MUA22_22 (Arabidopsis thaliana) AAM26644.1 (AY101523) Length = 508 Score = 30.4 bits (67), Expect = 3.5 Identities = 13/18 (72%), Positives = 13/18 (72%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFV GT   DP SLSM Sbjct: 173 IDPFVGGTS AA DPDSLSM 190 (SEQ ID NO: 75) >GBPLN: 18700120_18700121 AT5g14220/MUA22_22 (Arabidopsis thaliana) AAL77672.1 (AY075665) Length = 508 Score = 30.4 bits (67), Expect = 3.5 Identities = 13/18 (72%), Positives = 13/18 (72%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFV GT   DP SLSM Sbjct: 173 IDPFVGGTS AA DPDSLSM 190 (SEQ ID NO: 76) >GBPLN: 7573446_7573447 protoporphyrinogen oxidase-like protein (Arabidopsis thaliana) CAB87761.1 (AL163817) Length = 501 Score = 30.4 bits (67), Expect = 3.5 Identities = 13/18 (72%), Positives = 13/18 (72%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFV GT   DP SLSM Sbjct: 173 IDPFVGGTS AA DPDSLSM 190 (SEQ ID NO: 77) >GBPLN: 2564050_9757803 protoporphyrinogen IX oxidase (Arabidopsis thaliana BAB08301.1 (AB007650) Length = 547 Score = 30.4 bits (67), Expect = 3.5 Identities = 13/18 (72%), Positives = 13/18 (72%) Query: 1 IDPFVAGTCGGDPQSLSM 18 IDPFV GT   DP SLSM Sbjct: 219 IDPFVGGTS AA DPDSLSM 236 (SEQ ID NO: 78) Database: genbankpln0.aa Number of sequences in database: 607,682 Database: gbrefplant0.aa Number of sequences in database: 173,267 Lambda K H 0.319 0.141 0.455 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Hits to DB: 11,789,412 Number of Sequences: 780949 Number of extensions: 95485 Number of successful extensions: 181 Number of sequences better than 10.0: 25 Number of HSP's better than 10.0 without gapping: 22 Number of HSP's successfully gapped in prelim test: 3 Number of HSP's that attempted gapping in prelim test: 156 Number of HSP's gapped (non-prelim): 25 length of query: 18 length of database: 277,085,727 effective HSP length: 0 effective length of query: 18 X1: 16 (7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 64 (29.3 bits)

Complementation assays utilized a hemG (PPO) mutant strain of E. coli, SASX38 (Sasarman, 1979), to access the effect of the G210 deletion toward herbicide responses. The SASX38 strain grows very slowly unless supplied with exogenous heme or rescued with an alternative source of PPO. Furthermore, since wild type E. coli is naturally tolerant to PPO inhibitors, use of the SASX38 strain enabled a relatively direct assay for herbicide sensitivity of the S and R PPO2Ls from A. tuberculatus (Li, 2003; Sasarman, 1993). The SASX38 E. coli strain was transformed with plasmid constructs encoding PPO2L proteins differing only in the presence/absence of G210. Both constructs were able to rescue growth of the SASX38 E. coli strain, thus indicating both PPX2L genes encoded functional proteins (FIG. 6). However, supplementation of the growth medium with lactofen dramatically inhibited growth of E. coli transformed with the wild type PPX2L, but not E. coli transformed with the ΔG210 PPX2L (FIG. 6). Thus, the three-bp deletion in PPX2L resulting in deletion of a glycine at position 210 of PPO2L was sufficient to confer resistance to lactofen.

TABLE 1 Inheritance of resistance to the PPO inhibitor, lactofen, in A. tuberculatus. F₁ plants were obtained from reciprocal crosses between a resistant (R) and sensitive (S) biotype (F₁(R): female parent was R; F₁(S): female parent was S). Plants from F₂ and backcross lines were treated with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) COC, and scored as R or S 15 days after treatment. The expected segregation ratio of R to S responses assumes a single genetic unit of inheritance. Observed Expected Male Female numbers ratio P- parent parent N R S (R:S) χ² value F₁ (R) F₁ (R) 400 297 103 3:1 0.120 0.7290 S 200 98 102 1:1 0.080 0.7772 R 200 200 0 1:0 0 1 F₁ (S) F₁ (S) 400 304 96 3:1 0.213 0.6441 S 200 109 91 1:1 1.620 0.2030 R 200 200 0 1:0 0 1

TABLE 2 GR₅₀ (growth reduction by 50%) and degree of dominance^(b) estimates for PPO inhibitor-resistance in A. tuberculatus. Plants from R, S, F₁(R), or F₁(S) lines were treated with lactofen or acifluorfen, and data collected either 10 or 15 days after treatment (DAT). Dominance estimates are interpreted as: 0 to 1 = dominant; 0 = partially dominant; 0 to −1 = recessive. GR₅₀ R F₁(R) F₁(S) S Dominance DAT Herbicide (g ai ha⁻¹) F₁(R) F₁(S) 15 Lactofen 21 12 13 0.4 0.72 0.76 10 Acifluorfen 5.8 3.8 4.1 1.6 0.34 0.46 Lactofen 2.9 0.7 1.6 0.2 −0.06 0.56 ^(a)GR₅₀ estimates were calculated using PROC NLIN in SAS as described by Seefeldt et al. (1995). ^(b)The degree of dominance (D) = (2W₃ − W₂ − W₁)/(W₂ − W₁), where W₁ = log(GR₅₀) of the S-parent, W₂ = log(GR₅₀) or the R-parent, and W₃ = log(GR₅₀) of the F₁ lines (0 to 1 = dominant; 0 = partially dominant; 0 to −1 = recessive) (Stone 1968).

Numerous transformation vectors are available for plant transformation, and the genes of this invention can be used in conjunction with any such vectors. The selection of vector for use will depend upon the preferred transformation technique and the target species for transformation. For certain target species, different antibiotic or herbicide selection markers may be preferred. Selectable markers used routinely in transformation include the nptII gene which confers resistance to kanamycin and related antibiotics (Messing and Vierra. 1982. Gene 19: 259-268; Bevan et al. 1983. Nature 304:184-187), the bar gene which confers resistance to the herbicide phosphinothricin (White et al. 1990. Nucl Acids Res 18: 1062; Spencer et al. 1990. Theor Appl Genet 79: 625-631), the hph gene which confers resistance to the antibiotic hygromycin (Blochinger and Diggelmann. 1984. Mol Cell Biol 4: 2929-2931), and the dhfr gene, which confers resistance to methotrexate (Bourouis et al. 1983. EMBO J. 2(7): 1099-1104).

Many vectors are available for transformation using A. tumefaciens. These typically carry at least one T-DNA border sequence and include vectors such as pBIN19 (Bevan. 1984. Nucl. Acids Res.). Below the construction of two typical vectors is described. pCAMBIA vectors are well known to the art as well.

The exemplary binary vector pCIB10 contains a gene encoding kanamycin resistance for selection in plants, T-DNA right and left border sequences and incorporates sequences from the wide host-range plasmid pRK252 allowing it to replicate in both E. coli and Agrobacterium. Its construction is described by Rothstein et al. 1987. Gene 53: 153-161. Various derivatives of pCIB10 have been constructed which incorporate the gene for hygromycin B phosphotransferase described by Gritz et al. 1983. Gene 25: 179-188). These derivatives enable selection of transgenic plant cells on hygromycin only (pCIB743), or hygromycin and kanamycin (pCIB715, pCIB717). See, e.g., Rogers et al., Methods for Plant Molecular Biology, Weissbach and Weissbach, eds, Academic Press, San Diego, Calif., 1988, for a description of a kanamycin resistance marker. Other selective agents for use in plants include bleomycin, gentamicin and certain herbicide resistance markers (not via the PPX2L of the present invention).

Transformation without the use of A. tumefaciens circumvents the requirement for T-DNA sequences in the chosen transformation vector and consequently vectors lacking these sequences can be utilized in addition to vectors such as the ones described above which contain T-DNA sequences. Transformation techniques which do not rely on Agrobacterium include transformation via particle bombardment, protoplast uptake (e.g. PEG and electroporation) and microinjection. The choice of vector depends largely on the preferred selection for the species being transformed.

Gene sequences intended for expression in transgenic plants are first assembled in expression cassettes behind a suitable promoter and upstream of a suitable transcription terminator. These expression cassettes can then be easily transferred to the plant transformation vectors of choice.

The selection of a promoter used in expression cassettes determines the spatial and temporal expression pattern of the transgene in the transgenic plant. Selected promoters express transgenes in specific cell types (such as leaf epidermal cells, mesophyll cells, root cortex cells) or in specific tissues or organs (roots, leaves or flowers, for example), and this selection reflects the desired location of expression of the transgene. Alternatively, the selected promoter may drive expression of the gene under a light-induced or other temporally regulated promoter.

A variety of transcriptional terminators are available for use in expression cassettes. These are responsible for the termination of transcription beyond the transgene and its correct polyadenylation. Appropriate transcriptional terminators and those which are known to function in plants and include the CaMV 35S terminator, the tml terminator, the nopaline synthase (nos) terminator, the pea rbcS E9 terminator. These can be used in both monocotyledonous and dicotyledonous plants.

Numerous sequences have been found to enhance gene expression from within the transcriptional unit and these sequences can be used in conjunction with the genes of this invention to increase their expression in transgenic plants.

Various intron sequences have been shown to enhance expression, particularly in monocotyledonous cells. For example, the introns of the maize Adh1 gene significantly enhance the expression of the wild-type gene under its cognate promoter when introduced into maize cells. Intron 1 enhances expression in fusion constructs with the chloramphenicol acetyltransferase gene (Callis et al. 1987. Genes Develop. 1: 1183-1200). In the same experimental system, the intron from the maize bronzel gene had a similar effect in enhancing expression. Intron sequences have been routinely incorporated into plant transformation vectors, typically within the non-translated leader.

A number of non-translated leader sequences derived from viruses also enhance expression, especially in dicotyledonous cells. Leader sequences from Tobacco Mosaic Virus (TMV, the “W-sequence”), Maize Chlorotic Mottle Virus (MCMV), and Alfalfa Mosaic Virus (AMV) have been shown to enhance expression (e.g. Gallie et al. 1987. Nucl. Acids Res. 15: 8693-8711; Skuzeski et al. 1990. Plant Molec. Biol. 15:65-79).

While the herbicide resistant PPO of the present invention contains targeting sequences for chloroplast and mitochondria, various mechanisms for targeting gene products are known in plants; the sequences controlling the functioning of these mechanisms have been studied. Targeting of gene products to the chloroplast is controlled by a signal sequence at the N-terminus a protein; it is cleaved during chloroplast import to yield the mature protein (e.g. Comai et al. 1988. J. Biol. Chem. 263: 15104-15109). These signal sequences can be fused to heterologous gene products (lacking such sequences) to effect the import of heterologous products into the chloroplast (van den Broeck et al. 1985. Nature 313: 358-363). DNA encoding for appropriate signal sequences can be isolated from the 5′ end of the cDNAs encoding the RUBISCO protein, the CAB protein, the EPSP synthase enzyme, the GS2 protein and many other chloroplast-localized proteins.

Other gene products are localized to other organelles such as the mitochondrion and the peroxisome (e.g. Unger et al. 1989. Plant Molec. Biol. 13: 411-418). Sequences encoding these products can also be manipulated to effect the targeting of heterologous gene products to these organelles. Examples of such sequences are the nuclear-encoded ATPases and specific aspartate amino transferase isoforms for mitochondria. Targeting to cellular protein bodies has been described by Rogers et al. 1985. Proc. Natl. Acad. Sci. USA 82: 6512-6516).

In addition, sequences are known which target gene products to other cell compartments. N-terminal sequences are responsible for targeting to the ER, the apoplast, and extracellular secretion from aleurone cells (Koehler and Ho. 1990. Plant Cell 2: 769-783). Additionally, N-terminal sequences, in conjunction with C-terminal sequences, are responsible for vacuolar targeting (Shinshi et al. 1990. Plant Molec. Biol. 14: 357-368).

By the fusion of the appropriate targeting sequences described above to transgene sequences of interest it is possible to direct the transgene product to any organelle or cell compartment. For chloroplast targeting, for example, the chloroplast signal sequence from the RUBISCO gene, the CAB gene, the EPSP synthase gene, or the GS2 gene is fused in frame to the amino terminal ATG of the transgene. The signal sequence selected should include the known cleavage site and the fusion constructed should take into account any amino acids after the cleavage site which are required for cleavage. In some cases this requirement may be fulfilled by the addition of a small number of amino acids between the cleavage site and the transgene ATG or alternatively replacement of some amino acids within the transgene sequence. Fusions constructed for chloroplast import can be tested for efficacy of chloroplast uptake by in vitro translation of in vitro transcribed constructions followed by in vitro chloroplast uptake using techniques described by (Bartlett et al. In: Edelmann et al. (Eds.) Methods in Chloroplast Molecular Biology, Elsevier, pp 1081-1091, 1982; Wasmann et al. 1986. Mol. Gen. Genet. 205: 446-453). These construction techniques are well known in the art and are equally applicable to mitochondria and peroxisomes. The choice of targeting which may be required for expression of the transgenes will depend on the cellular localization of the precursor required as the starting point for a given pathway. This will usually be cytosolic or chloroplastic, although it may is some cases be mitochondrial or peroxisomal. The products of transgene expression will not normally require targeting to the ER, the apoplast or the vacuole.

The above described mechanisms for cellular targeting can be utilized not only in conjunction with their cognate promoters, but also in conjunction with heterologous promoters so as to effect a specific targeting goal (where the heterologous promoter has an expression pattern different to that of the promoter from which the targeting signal is derived).

Agrobacterium-mediated transformation is a preferred technique for transformation of dicots because of the high efficiency of transformation and success with many different species. The many crop species which are routinely transformable by Agrobacterium include tobacco, tomato, sunflower, cotton, oilseed rape, potato, soybean, alfalfa and poplar (EP 317 511, cotton; EP 0 249 432, tomato, to Calgene; WO 87/07299, Brassica, to Calgene; U.S. Pat. No. 4,795,855, poplar). Agrobacterium transformation typically involves the transfer of the binary vector carrying the foreign DNA of interest to an appropriate Agrobacterium strain which may depend of the complement of vir genes carried by the host Agrobacterium strain either on a co-resident Ti plasmid or chromosomally (e.g. strain CIB542 for pCIB200 and pCIB2001 (Uknes et al. 1993. Plant Cell 5: 159-169). The transfer of the recombinant binary vector to Agrobacterium is accomplished by a triparental mating procedure using E. coli carrying the recombinant binary vector, a helper E. coli strain which carries a plasmid such as pRK2013 and which is able to mobilize the recombinant binary vector to the target Agrobacterium strain. Alternatively, the recombinant binary vector can be transferred to Agrobacterium by DNA transformation (Hofgen and Willmitzer. 1988. Nucl. Acids Res. 16: 9877).

Once an expression construct or expression vector of the invention has been established, it can be transformed into a plant cell. A variety of methods for introducing nucleic acid sequences (e.g., vectors) into the genome of plants and for the regeneration of plants from plant tissues or plant cells are known (Plant Molecular Biology and Biotechnology (CRC Press, Boca Raton, Fla., pp. 71-119 (1993); White F F. 1993. Vectors for Gene Transfer in Higher Plants; in: Transgenic Plants, vol. 1, Engineering and Utilization, Ed.: Kung and Wu R, Academic Press, 15-38; Jenes et al. 1993. Techniques for Gene Transfer, in: Transgenic Plants, vol. 1, Engineering and Utilization, Ed.: Kung and R. Wu, Academic Press, pp. 128-143; Potrykus et al. 1991. Annu. Rev. Plant Physiol. Plant Molec. Biol. 42:205-225; Halford and Shewry. 2000. Br. Med. Bull. 56:62-73).

Transformation methods may include direct and indirect methods of transformation. Suitable direct methods include polyethylene glycol induced DNA uptake, liposome-mediated transformation (U.S. Pat. No. 4,536,475), biolistic methods using the gene gun (particle bombardment; Fromm et al. 1990. Bio/Technology. 8:833-9; Gordon-Kamm et al. 1990. Plant Cell 2:603), electroporation, incubation of dry embryos in DNA-comprising solution, and microinjection. In the case of these direct transformation methods, the plasmid used need not meet any particular requirements. Simple plasmids, such as those of the pUC series, pBR322, M13 mp series, pACYC184 and the like can be used. If intact plants are to be regenerated from the transformed cells, an additional selectable marker gene is preferably located on the plasmid. The direct transformation techniques are equally suitable for dicotyledonous and monocotyledonous plants.

Transformation can also be carried out by bacterial infection by means of Agrobacterium (for example EP 116,718), viral infection by means of viral vectors (EP 067,553; U.S. Pat. No. 4,407,956; WO 95/34668; WO 93/03161) or by means of pollen (EP 270,356; WO 85/01856; U.S. Pat. No. 4,684,611). Agrobacterium based transformation techniques (especially for dicotyledonous plants) are well known in the art. The Agrobacterium strain (e.g., Agrobacterium tumefaciens or Agrobacterium rhizogenes) comprises a plasmid (Ti or Ri plasmid) and a T-DNA element which is transferred to the plant following infection with Agrobacterium. The T-DNA (transferred DNA) is integrated into the genome of the plant cell. The T-DNA may be localized on the Ri- or Ti-plasmid or is separately comprised in a so-called binary vector. Methods for the Agrobacterium-mediated transformation are described, for example, in Horsch R B et al. 1985. Science 225:1229f. The Agrobacterium-mediated transformation is best suited to dicotyledonous plants but has also been adapted to monocotyledonous plants. The transformation of plants by Agrobacteria is described, for example, in White F F, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1, Engineering and Utilization, edited by S. D. Kung and R. Wu, Academic Press, 1993, pp. 15-38; Jenes B et al. 1993. Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineering and Utilization, edited by S. D. Kung and R. Wu, Academic Press, pp. 128-143; Potrykus 1991. Annu Rev Plant Physiol Plant Molec Biol 42:205-225).

Transformation may result in transient or stable transformation and expression; stable transformation is preferred in the practice of the present invention. Although a nucleotide sequence of the present invention can be inserted into any plant and plant cell, it is particularly useful in crop plant cells. Alternatively, the herbicide resistance deletion mutation can be introduced into plant cells and the mutation paced in the genome via homologous recombination of a recombinagenic oligonucleotide carrying the deletion of appropriate codon, with about 10 to about 70 flanking nucleotides on either side of the deletion, with the flanking nucleotides matched to the genomic sequence on either side of the codon to be deleted.

Various tissues are suitable as starting material (explant) for the Agrobacterium-mediated transformation process including but not limited to callus (U.S. Pat. No. 5,591,616; EP 604 662), immature embryos (EP 672 752), pollen (U.S. Pat. No. 5,929,300), shoot apex (U.S. Pat. No. 5,164,310), or in planta transformation (U.S. Pat. No. 5,994,624). The method and material described herein can be combined with virtually all Agrobacterium mediated transformation methods known in the art. Preferred combinations include, but are not limited, to the following starting materials and methods:

Variety Material/Citation Monocotyledonous Immature embryos (EP-A1 672 752) plants: Callus (EP-A1 604 662) Embryogenic callus (U.S. Pat. No. 6,074,877) Inflorescence (U.S. Pat. No. 6,037,522) Flower (in planta) (WO 01/12828) Banana U.S. Pat. No. 5,792,935; EP 731 632; U.S. Pat. No. 6,133,035 Barley WO 99/04618 Maize U.S. Pat. No. 5,177,010; U.S. Pat. No. 5,987,840 Pineapple U.S. Pat. No. 5,952,543; WO 01/33943 Rice EP 897 013; U.S. Pat. No. 6,215,051; WO 01/12828 Wheat AU 738 153; EP 856 060 Beans U.S. Pat. No. 5,169,770; EP 397 687 Brassica U.S. Pat. No. 5,188,958; EP 270 615; EP-A1 1,009,845 Cacao U.S. Pat. No. 6,150,587 Citrus U.S. Pat. No. 6,103,955 Coffee AU 729 635 Cotton U.S. Pat. No. 5,004,863; EP-A1 270 355; U.S. Pat. No. 5,846,797; EP-A1 1,183,377; EP-A1 1,050,334; EP-A1 1,197,579; EP-A1 1,159,436 Pollen transformation (U.S. Pat. No. 5,929,300) In planta transformation (U.S. Pat. No. 5,994,624) Pea U.S. Pat. No. 5,286,635 Pepper U.S. Pat. No. 5,262,316 Poplar U.S. Pat. No. 4,795,855 Soybean cotyledonary node of germinated soybean seedlings shoot apex (U.S. Pat. No. 5,164,310) axillary meristematic tissue of primary, or higher leaf node of about 7 days germinated soybean seedlings organogenic callus cultures dehydrated embryo axes U.S. Pat. No. 5,376,543; EP 397 687; U.S. Pat. No. 5,416,011; U.S. Pat. No. 5,968,830; U.S. Pat. No. 5,563,055; U.S. Pat. No. 5,959,179; EP 652 965; EP 1,141,346 Sugarbeet EP 517 833; WO 01/42480 Tomato U.S. Pat. No. 5,565,347

In another embodiment, a nucleotide sequence of the present invention is directly transformed into the plastid genome. Plastid expression, in which genes are inserted by homologous recombination into the several thousand copies of the circular plastid genome present in each plant cell, takes advantage of the enormous copy number advantage over nuclear-expressed genes to permit high expression levels. In a preferred embodiment, the nucleotide sequence is inserted into a plastid targeting vector and transformed into the plastid genome of a desired plant host. Plants homoplasmic for plastid genomes containing the nucleotide sequence are obtained, and are preferentially capable of high expression of the nucleotide sequence.

Plastid transformation technology is, for example, extensively described in U.S. Pat. Nos. 5,451,513; 5,545,817; 5,545,818; and 5,877,462; in WO 95/16783 and WO 97/32977; and in McBride et al. 1994. Proc. Natl. Acad. Sci. USA 91: 7301-7305, all incorporated herein by reference in their entireties. The basic technique for plastid transformation involves introducing regions of cloned plastid DNA flanking a selectable marker together with the nucleotide sequence into a suitable target tissue, e.g., using biolistic or protoplast transformation (e.g., calcium chloride or PEG mediated transformation). The 1 to 1.5 kb flanking regions, termed targeting sequences, facilitate homologous recombination with the plastid genome and thus allow the replacement or modification of specific regions of the plastome. Initially, point mutations in the chloroplast 16S rRNA and rps12 genes conferring resistance to spectinomycin and/or streptomycin are utilized as selectable markers for transformation (Svab et al. 1990 Proc. Natl. Acad. Sci. USA 87: 8526-8530; Staub et al. (1992) Plant Cell 4, 39-45). The presence of cloning sites between these markers allowed creation of a plastid targeting vector for introduction of foreign genes (Staub et al. 1993. EMBO J. 12: 601-606). Substantial increases in transformation frequency are obtained by replacement of the recessive rRNA or r-protein antibiotic resistance genes with a dominant selectable marker, the bacterial aadA gene encoding the spectinomycin-detoxifying enzyme aminoglycoside-3′-adenyltransferase (Svab et al. 1993. Proc. Natl. Acad. Sc. USA 90: 913-917). Other selectable markers useful for plastid transformation are known in the art and encompassed within the scope of the invention. However, in the context of the present invention, the use of nuclear herbicide resistance gene is preferred, especially when expression is achieved in plastids as well as cytoplasm, and if a marker is used which confers herbicide resistance, there should be no cross resistance between that marker and the herbicide resistant PPO of the present invention.

For using the methods according to the invention, the skilled worker has available well-known tools, such as expression vectors with promoters which are suitable for plants, and methods for the transformation and regeneration of plants.

To select cells which have successfully undergone transformation, it is preferred to introduce a selectable marker which confers, to the cells which have successfully undergone transformation, a resistance to a biocide (for example a herbicide), a metabolism inhibitor such as 2-deoxyglucose-6-phosphate (WO 98/45456) or an antibiotic. The selection marker permits the transformed cells to be selected from untransformed cells (McCormick et al. 1986. Plant Cell Reports 5:81-84). Suitable selection markers are described above and includes antibiotic resistance markers, among others.

Transgenic plants can be regenerated in the known manner from the transformed cells. The resulting plantlets can be planted and grown in the customary manner. Preferably, two or more generations should be cultured to ensure that the genomic integration is stable and hereditary. Suitable methods are described (Fennell et al. 1992. Plant Cell Rep. 11: 567-570; Stoeger et al. 1995. Plant Cell Rep. 14:273-278; Jahne et al. 1994. Theor Appl Genet 89:525-533).

Transformation of most monocotyledon species has now also become routine. Preferred techniques include direct gene transfer into protoplasts using PEG or electroporation techniques, and particle bombardment into callus tissue. Transformations can be undertaken with a single DNA species or multiple DNA species (i.e., co-transformation) and both these techniques are suitable for use with this invention. Co-transformation may have the advantage of avoiding complex vector construction and of generating transgenic plants with unlinked loci for the gene of interest and the selectable marker, enabling the removal of the selectable marker in subsequent generations, should this be regarded desirable. However, a disadvantage of the use of co-transformation is the less than 100% frequency with which separate DNA species are integrated into the genome (Schocher et al. 1986. Biotechnology 4: 1093-1096). EP 0 292 435, EP 0 392 225 and WO 93/07278 describe techniques for the preparation of callus and protoplasts from an elite inbred line of maize, transformation of protoplasts using PEG or electroporation, and the regeneration of maize plants from transformed protoplasts. Gordon-Kamm et al. 1990. Plant Cell 2: 603-618 and Fromm et al. 1990. Biotechnology 8: 833-839 have published techniques for transformation of A188-derived maize line using particle bombardment. Furthermore, WO 93/07278 and Koziel et al. 1993. Biotechnology 11: 194-200 describe techniques for the transformation of elite inbred lines of maize by particle bombardment. This technique utilizes immature maize embryos of 1.5-2.5 mm length excised from a maize ear 14-15 days after pollination and a biolistics device for bombardment.

Transformation of rice can also be undertaken by direct gene transfer techniques utilizing protoplasts or particle bombardment. Protoplast-mediated transformation has been described for Japonica-types and Indica-types (Zhang et al. 1988. Plant Cell Rep 7: 379-384; Shimamoto et al. 1989. Nature 338: 274-277; Datta et al. 1990. Biotechnology 8: 736-740). Both types are also routinely transformable using particle bombardment (Christou et al. 1991. Biotechnology 9: 957-962).

EP 332 581 describes techniques for the generation, transformation and regeneration of Pooideae protoplasts. These techniques allow the transformation of Dactylis and wheat. Furthermore, wheat transformation was been described by Vasil et al. 1992. Biotechnology 10: 667-674) using particle bombardment into cells of type C long-term regenerable callus, and also by Vasil et al. 1993. Biotechnology 11: 1553-1558 and Weeks et al. 1993. Plant Physiol. 102: 1077-1084 using particle bombardment of immature embryos and immature embryo-derived callus. A preferred technique for wheat transformation, however, involves the transformation of wheat by particle bombardment of immature embryos and includes either a high sucrose or a high maltose step prior to gene delivery. Prior to bombardment, any number of embryos (0.75-1 mm in length) are plated onto MS medium with 3% sucrose (Murashige and Skoog. 1962. Physiologia Plantarum 15: 473-497) and 3 mg/l 2,4-D for induction of somatic embryos which is allowed to proceed in the dark. On the chosen day of bombardment, embryos are removed from the induction medium and placed onto the osmoticum (i.e. induction medium with sucrose or maltose added at the desired concentration, typically 15%). The embryos are allowed to plasmolyze for 2-3 h and are then bombarded. Twenty embryos per target plate is typical, although not critical. An appropriate gene-carrying plasmid (such as pCIB3064 or pSG35) is precipitated onto micrometer size gold particles using standard procedures. Each plate of embryos is shot with the DuPont Biolistics, helium device using a burst pressure of .about.1000 psi using a standard 80 mesh screen. After bombardment, the embryos are placed back into the dark to recover for about 24 h (still on osmoticum). After 24 hrs, the embryos are removed from the osmoticum and placed back onto induction. medium where they stay for about a month before regeneration. Approximately one month later the embryo explants with developing embryogenic callus are transferred to regeneration medium (MS+1 mg/liter NAA, 5 mg/liter GA), further containing the appropriate selection agent (10 mg/l basta in the case of pCIB3064 and 2 mg/l methotrexate in the case of pSOG35). After approximately one month, developed shoots are transferred to larger sterile containers known as “GA7s” which contained half-strength MS, 2% sucrose, and the same concentration of selection agent. U.S. patent application Ser. No. 08/147,161 describes methods for wheat transformation.

Resistant mutant plasmids, selected for resistance against a single herbicide, are tested against a spectrum of other protox-inhibiting compounds. A strain containing the wild-type plasmid is plated on a range of concentrations of each compound to determine the lethal concentration for each one. Resistant mutant plasmids in the same genetic background are plated and scored for the ability to survive on a concentration of each compound which is at least 10 fold higher than the concentration that is lethal to the strain containing the wild-type plasmid.

The herbicide resistant PPO isolated from waterhemp confers the resistant phenotype to transformed E. coli, and it likewise confers the resistant phenotype to transgenic plants into which it has been introduced. Table 4 gives the consensus amino acid sequence derived from at least three specific examples of a PPX2L sequence. Unlike various herbicide resistant mutants previously described (see, e.g., U.S. Pat. Nos. 6,282,837; 5,939,602; and 6,808,904), the present resistant mutants have undergone a spontaneous deletion mutation such that where there was Gly-Gly, there is now only one Gly residue (wild type Gly-Gly at amino acids 210-211 of SEQ ID NO:16). The PPO mutant coding sequence in Table 4 only varies from the wild type in the deletion of a Gly codon; the PPO amino acid sequence depicted in Table 4 et seq. further contain an amino acid substitution at residue Gln for Arg at position 182 and Cys for Ser at position 448. See also FIGS. 10A-10B for additional polymorphisms. Without wishing to be bound by any particular theory, the present inventors believe that the Gly deletion alone is sufficient to confer the herbicide resistant phenotype. Thus the wild type sequence can be modified only to effect the Gly-Gly to Gly mutation, or it can include one or the other of the substitutions in addition to the Gly deletion, with the result of conferring resistant to herbicides, as described herein. Expression of any of these Gly-deleted enzymes in a transgenic plant results in a plant with robust resistance to herbicides.

As an alternative to genetic modification of a crop of interest, the herbicide resistant PPO gene of the present invention can be introduced into cultivated amaranth species by conventional plant breeding (crossing the resistant weed with the crop, selecting for herbicide resistant progeny with the desired crop characteristics, and then backcrossing for three to ten cycles progeny plants to the crop species, selecting for herbicide resistance and crop characteristics) to produce the resistant crop. Amaranthus species which are cultivated as crops include, but are not limited to, A. hypochondriacus, A. cruentus, A. caudatus, A. dubius, and A. tricolor.

The amino acids which occur in the various amino acid sequences referred to in the specification have their usual three- and one-letter abbreviations routinely used in the art: A, Ala, Alanine; C, Cys, Cysteine; D, Asp, Aspartic Acid; E, Glu, Glutamic Acid; F, Phe, Phenylalanine; G, Gly, Glycine; H, His, Histidine; I, Ile, Isoleucine; K, Lys, Lysine; L, Leu, Leucine; M, Met, Methionine; N, Asn, Asparagine; P, Pro, Proline; Q, Gln, Glutamine; R, Arg, Arginine; S, Ser, Serine; T, Thr, Threonine; V, Val, Valine; W, Try, Tryptophan; Y, Tyr, Tyrosine.

A protein is considered an isolated protein if it is a protein isolated from or produced in a host cell in which it is recombinantly produced. It can be purified or it can simply be free of other proteins and biological materials with which it is associated in nature.

A transgenic plant is one which contains and expresses a gene (or transgene) which it does not contain and express in nature. The transgene can be a gene found in the particular plant but altered in the laboratory to be covalently attached to sequences which it does not occur in nature, the gene can have been altered in the laboratory to have a particular sequence of interest or to have a particular function that it did not previously, or the gene can have been isolated from a mutant plant of the same species and introduced into the genome of a plant of that species, which plant had not had that particular gene or sequence. Progeny transgenic plants are offspring (and succeeding generations of offspring which contain and express a copy of the transgene of interest. Transgenic seed are those produced by a transgenic plant or progeny transgenic plant which contain the transgene of interest.

Expression directed by a particular sequence means there is transcription and translation of an associated downstream sequence. With reference to tissue-specific regulation of expression of a PPO sequence of interest operably linked to the plant-expressible transcription regulatory sequence, expression may be advantageously determined by a strong constitutive promoter such as the Cauliflower Mosaic Virus 19S or 35 S promoter, a tandem repeat 35S promoter, the actin 2 promoter from Arabidopsis thaliana, among others.

A transcription regulatory sequence includes a promoter sequence and the cis-active sequences necessary for regulated expression of the operably linked sequence in the desired plant tissues. A promoter includes sequences sufficient to cause transcription of an associated (downstream, operably linked) sequence. The promoter is desirably constitutive, or it may be regulated, e.g., inducible, the transcription regulatory sequences cause expression of the operably linked coding sequence in response to an environmental signal (light, chemical, cold, heat, etc).

One DNA portion or sequence is downstream of second DNA portion or sequence when it is located 3′ of the second sequence. One DNA portion or sequence is upstream of a second DNA portion or sequence when it is located 5′ of that sequence.

One DNA molecule or sequence and another are heterologous to another if the two are not derived from the same ultimate natural source. The sequences may be natural sequences, or at least one sequence can be designed by man, as in the case of a multiple cloning site region. The two sequences can be derived from two different species or one sequence can be produced by chemical synthesis provided that the nucleotide sequence of the synthesized portion was not derived from the same organism as the other sequence.

An isolated or substantially pure nucleic acid molecule or polynucleotide is a polynucleotide which is substantially separated from other polynucleotide sequences which naturally accompany a native herbicide resistant PPO coding sequence. This coding sequence may be operably linked to its native transcription regulatory sequences or another native transcription regulatory sequence functional in a plant cell. The term embraces a polynucleotide sequence which has been removed from its naturally occurring environment, and includes recombinant or cloned DNA isolates, chemically synthesized analogues and analogues biologically synthesized by heterologous systems.

A polynucleotide is said to encode a polypeptide if, in its native state or when manipulated by methods known to those skilled in the art, it can be transcribed and/or translated to produce the polypeptide or a fragment thereof. The anti-sense strand of such a polynucleotide is also said to encode the sequence.

A nucleotide sequence is operably linked when it is placed into a functional relationship with another nucleotide sequence. For instance, a promoter is operably linked to a coding sequence if the promoter effects its transcription or expression. Generally, operably linked means that the sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame. However, it is well known that certain genetic elements, such as enhancers, may be operably linked even at a distance, i.e., even if not contiguous.

The term recombinant polynucleotide refers to a polynucleotide which is made by the combination of two otherwise separated segments of sequence accomplished by the artificial manipulation of isolated segments of polynucleotides by genetic engineering techniques or by chemical synthesis. In so doing one may join together polynucleotide segments of desired functions to generate a desired combination of functions.

Polynucleotide probes include an isolated polynucleotide attached to a label or reporter molecule and may be used to identify and isolate other PPO coding sequences or other transcriptional regulatory sequences. Probes comprising synthetic oligonucleotides or other polynucleotides may be derived from naturally occurring or recombinant single or double stranded nucleic acids or be chemically synthesized. Polynucleotide probes may be labeled by any of the methods known in the art, e.g., random hexamer labeling, nick translation, or the Klenow fill-in reaction.

Large amounts of the polynucleotides may be produced by replication in a suitable host cell. Natural or synthetic DNA fragments coding for a protein of interest are incorporated into recombinant polynucleotide constructs, typically DNA constructs, capable of introduction into and replication in a prokaryotic or eukaryotic cell, especially Escherichia coli, wherein protein expression is desired or in a PPO-deficient strain of Escherichia coli when testing of PPO activity and/or herbicide resistance is desired. Commonly used prokaryotic hosts include strains of Escherichia coli, although other prokaryotes, such as Bacillus subtilis or a pseudomonad, may also be used. Eukaryotic host cells can include various plant species such as Arabidopsis thaliana, Nicotiana tabacum, Glycine max, Zea mays, Medicago, yeast, filamentous fungi, plant, insect, amphibian and avian species.

The polynucleotides of interest may also be produced by chemical synthesis, e.g., by the phosphoramidite method described by Beaucage and Caruthers (1981) Tetra. Letts. 22: 1859-1862 or the triester method according to Matteuci et al. (1981) J. Am. Chem. Soc. 103: 3185, and may be performed on commercial automated oligonucleotide synthesizers. A double-stranded fragment may be obtained from the single stranded product of chemical synthesis either by synthesizing the complementary strand and annealing the strand together under appropriate conditions or by adding the complementary strand using DNA polymerase with an appropriate primer sequence.

DNA constructs prepared for introduction into a prokaryotic or eukaryotic host will typically comprise a replication system (i.e. vector) recognized by the host, including the intended DNA fragment encoding the desired polypeptide, and will preferably also include transcription and translational initiation regulatory sequences operably linked to the polypeptide-encoding segment. Expression systems (expression vectors) may include, for example, an origin of replication or autonomously replicating sequence (ARS) and expression control sequences, a promoter, an enhancer and necessary processing information sites, such as ribosome-binding sites, RNA splice sites, polyadenylation sites, transcriptional terminator sequences, and mRNA stabilizing sequences. Signal peptides may also be included where appropriate from secreted polypeptides of the same or related species, which allow the protein to cross and/or lodge in cell membranes or be secreted from the cell.

An appropriate promoter and other necessary vector sequences will be selected so as to be functional in the host. Examples of workable combinations of cell lines and expression vectors are described in Sambrook et al. (1989) vide infra; Ausubel et al. (Eds.) (1999) Short Protocols in Molecular Biology, fourth edition, Wiley and Sons, New York; and Metzger et al. (1988) Nature, 334: 31-36. Many useful vectors for expression in bacteria, yeast, fungal, mammalian, insect, plant or other cells are well known in the art and may be obtained such vendors as Clontech, Invitrogen, Stratagene, New England Biolabs, Promega and others. In addition, the construct may be joined to an amplifiable gene (e.g., DHFR) so that multiple copies of the gene may be made. For appropriate enhancer and other expression control sequences, see also Enhancers and Eukaryotic Gene Expression, Cold Spring Harbor Press, N.Y. (1983). While such expression vectors may replicate autonomously, they may less preferably replicate by being inserted into the genome of the host cell.

Expression and cloning vectors likely contain a selectable marker, that is, a gene encoding a protein necessary for the survival or growth of a host cell transformed with the vector. Although such a marker gene may be carried on another polynucleotide sequence co-introduced into the host cell, it is most often contained on the cloning or expression vector. Only those host cells into which the marker gene has been introduced will survive and/or grow under selective conditions. Typical selection genes encode proteins that confer resistance to antibiotics or other toxic substances, e.g., ampicillin, neomycin, methotrexate, etc.; complement auxotrophic deficiencies; or supply critical nutrients not available from complex media. The choice of the proper selectable marker depends on the host cell; appropriate markers for different hosts are known in the art.

Recombinant host cells, in the present context, are those which have been genetically modified to contain and express an isolated DNA molecule of the instant invention. The DNA can be introduced by any means known to the art which is appropriate for the particular type of cell, including without limitation, transformation, lipofection, microinjection, Agro-infection, electroporation or particle bombardment.

It is recognized by those skilled in the art that the DNA sequences may vary due to the degeneracy of the genetic code and codon usage. All DNA sequences which code for the specifically exemplified herbicide resistant PPO having the particular glycine deletion taught herein are included in this invention, including the DNA sequence as given in Table 3, as well as functional equivalents thereto including or lacking substitution mutations as further taught herein.

Additionally, it is recognized by those skilled in the art that allelic variations occur in the DNA sequences which do not significantly change activities of the proteins they encode. All synonymous and functionally equivalent DNA sequences are included within the scope of this invention. The skilled artisan understands that the sequence of the exemplified herbicide resistant PPO sequences can be used to identify and isolate additional, nonexemplified nucleotide sequences which are functionally equivalent to the sequences given in SEQ ID NO:13, 25, 29 and 45, including naturally occurring variations in PPX2L sequences.

Hybridization and/or polymerase chain reaction procedures are useful for identifying polynucleotides with sufficient homology to the subject regulatory sequences to be useful as taught herein. The particular hybridization technique is not essential to the subject invention. As improvements are made in hybridization techniques, they can be readily applied by one of ordinary skill in the art.

A probe and sample are combined in a hybridization buffer solution and held at an appropriate temperature until annealing occurs. Thereafter, the membrane is washed free of extraneous materials, leaving the sample and bound probe molecules typically detected and quantified by autoradiography and/or liquid scintillation counting. As is well known in the art, if the probe molecule and nucleic acid sample hybridize by forming a strong non-covalent bond between the two molecules, it can be reasonably assumed that the probe and sample are essentially identical, or completely complementary, if the annealing and washing steps are carried out under conditions of high stringency. The probe's detectable label provides a means for determining whether hybridization has occurred.

In the use of the oligonucleotides or polynucleotides as probes, the particular probe is labeled with any suitable label known to those skilled in the art, including radioactive and non-radioactive labels. Typical radioactive labels include ³²P, ³⁵S, or the like. Non-radioactive labels include, for example, ligands such as biotin or thyroxine, as well as enzymes such as hydrolases or peroxidases, or a chemiluminescer such as luciferin, or fluorescent compounds like fluorescein and its derivatives. Alternatively, the probes can be made inherently fluorescent as described in WO 93/16094.

Various degrees of stringency of hybridization can be employed. The more stringent the conditions, the greater the complementarity required for duplex formation. Stringency can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under moderate to high stringency conditions by techniques well know in the art, as described, for example in Keller, G. H., M. M. Manak (1987) DNA Probes, Stockton Press, New York, N.Y., pp. 169-170.

As used herein, moderate to high stringency conditions for hybridization are conditions which achieve the same, or about the same, degree of specificity of hybridization as the conditions employed by the current inventors. An example of high stringency conditions are hybridizing at 68° C. in 5×SSC/5×Denhardt's solution/0.1% SDS, and washing in 0.2×SSC/0.1% SDS at room temperature. An example of conditions of moderate stringency are hybridizing at 68° C. in 5×SSC/5×Denhardt's solution/0.1% SDS and washing at 42° C. in 3×SSC. The parameters of temperature and salt concentration can be varied to achieve the desired level of sequence identity between probe and target nucleic acid. See, e.g., Sambrook et al. (1989) vide infra or Ausubel et al. (1995) Current Protocols in Molecular Biology, John Wiley & Sons, NY, N.Y., for further guidance on hybridization conditions.

Specifically, hybridization of immobilized DNA in Southern blots with ³²P-labeled gene specific probes was performed by standard methods (Maniatis et al.) In general, hybridization and subsequent washes were carried out under moderate to high stringency conditions that allowed for detection of target sequences with homology to the exemplified PPO sequences. For double-stranded DNA gene probes, hybridization can be carried out overnight at 20-25° C. below the melting temperature (Tm) of the DNA hybrid in 6×SSPE 5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. The melting temperature is described by the following formula (Beltz, G. A et al. (1983) Meth. Enzymol. R. Wu, et al. (eds.) Academic Press, New York 100:266-285).

Tm=81.5° C.+16.6 Log(Na+)+0.41(+G+C)−0.61(% formamide)-600/length of duplex in base pairs.

Washes are typically carried out as follows: twice at room temperature for 15 minutes in 1×SSPE, 0.1% SDS (low stringency wash), and once at TM-20° C. for 15 minutes in 0.2×SSPE, 0.1% SDS (moderate stringency wash).

For oligonucleotide probes, hybridization was carried out overnight at 10-20° C. below the melting temperature (Tm) of the hybrid 6×SSPE, 5×Denhardt's solution, 0.1% SDS, 0.1 mg/ml denatured DNA. Tm for oligonucleotide probes was determined by the following formula: TM(° C.)=2(number T/A base pairs+4(number G/C base pairs) (Suggs, S. V. et al. (1981) ICB-UCLA Symp. Dev. Biol. Using Purified Genes, D. D. Brown (ed.), Academic Press, New York, 23:683-693).

Washes were typically carried out as follows: twice at room temperature for 15 minutes 1×SSPE, 0.1% SDS (low stringency wash), and once at the hybridization temperature for 15 minutes in 1×SSPE, 0.1% SDS (moderate stringency wash).

In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment>70 or so bases in length, the following conditions can be used: Low, 1 or 2×SSPE, room temperature; Low, 1 or 2×SSPE, 42° C.; Moderate, 0.2× or 1×SSPE, 65° C.; and High, 0.1×SSPE, 65° C.

Duplex formation and stability depend on substantial complementarity between the two strands of a hybrid, and, as noted above, a certain degree of mismatch can be tolerated. Therefore, the probe sequences of the subject invention include mutations (both single and multiple), deletions, insertions of the described sequences, and combinations thereof, wherein said mutations, insertions and deletions permit formation of stable hybrids with the target polynucleotide of interest. Mutations, insertions, and deletions can be produced in a given polynucleotide sequence in many ways, and those methods are known to an ordinarily skilled artisan.

Polymerase Chain Reaction (PCR) is a repetitive, enzymatic, primed synthesis and amplification of a nucleic acid sequence. This procedure is well known and commonly used by those skilled in this art (see, e.g., Mullis, U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,800,159; Saiki et al. 1985. Science 230:1350-1354). Kits and reagents are readily available from commercial sources. The skilled artisan can routinely produce deletion-, insertion-, or substitution-type mutations and identify those resulting mutants which contain the desired characteristics of the specifically exemplified sequences, i.e., those which retain herbicide resistance and PPX2L activity, although other means for making mutations in a particular sequence are known to the art. Methods for confirming herbicide resistance and PPO activity are known in the art.

DNA sequences having at least 85, 90, 95%, and all integers from 85 to 99%, identity to the recited DNA sequences of Tables 3 and 5 and functioning to encode an herbicide resistant PPO are considered the most preferred equivalents to these sequences. Such functional equivalents are included in the definition of an herbicide resistant PPO coding sequence. Following the teachings herein and using knowledge and techniques well known in the art, the skilled worker will be able to make a large number of operative embodiments having equivalent DNA sequences to those listed herein without the expense of undue experimentation.

As used herein percent sequence identity of two nucleic acids is determined using the algorithm of Karlin and Altschul. 1990. Proc. Natl. Acad. Sci. USA 87:2264-2268, modified as in Karlin and Altschul. 1993. Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. 1990. J. Mol. Biol. 215:402-410. BLAST nucleotide searches are performed with the NBLAST program, score=100, wordlength=12, to obtain nucleotide sequences with the desired percent sequence identity. To obtain gapped alignments for comparison purposes, Gapped BLAST is used as described in Altschul et al. 1997. Nucl. Acids. Res. 25:3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (NBLAST and XBLAST) are used. See the National Center for Biotechnology Information website.

The choice of vector in which the DNA of interest is inserted depends, as is well known in the art, on the functional properties desired, e.g., replication, protein expression, and the host cell to be transformed. The vector desirably includes a prokaryotic replicon, i.e., a DNA sequence having the ability to direct autonomous replication and maintenance of the recombinant DNA molecule extra-chromosomally when introduced into a prokaryotic host cell, such as a bacterial host cell. Such replicons are well known in the art. In addition, preferred embodiments that include a prokaryotic replicon also include a gene whose expression confers a selective advantage, such as a drug resistance, to the bacterial host cell when introduced into those transformed cells. Typical bacterial drug resistance genes are those that confer resistance to ampicillin or tetracycline, among other selective agents. The neomycin phosphotransferase gene has the advantage that it is expressed in eukaryotic as well as prokaryotic cells; others are well known.

Those vectors that include a prokaryotic replicon also typically include convenient restriction sites for insertion of a recombinant DNA molecule of the present invention; such vectors include pUC8, pUC9, pBR322, and pBR329. Vectors are available from BioRad Laboratories (Richmond, Calif.), Pharmacia (Piscataway, N.J.), Stratagene (La Jolla, Calif.), Promega Corporation, Madison, Wis., and many other commercial sources. The vector may also be a Lambda phage vector; see. e.g. Molecular Cloning: A Laboratory Manual, Second Edition, Maniatis et al., eds., Cold Spring Harbor Press (1989) and commercial sources. Other exemplary vectors include pCMU (Nilsson et al. (1989) Cell 58:707) and derivatives.

Typical expression vectors capable of expressing a recombinant nucleic acid sequence in plant cells and capable of directing stable integration within the host plant cell include vectors derived from the tumor-inducing (Ti) plasmid of A. tumefaciens described by Rogers et al. 1987. Meth. Enzymol. 153:253-277, and several other expression vector systems known to function in plants. See for example, WO87/00551; Cocking and Davey. 1987. Science 236:1259-1262.

A transgenic plant can be produced by any means known to the art, including but not limited to A. tumefaciens-mediated DNA transfer, Agrobacterium rhizogenes-mediated DNA transfer, both preferably with a disarmed T-DNA vector, electroporation, direct DNA transfer, liposomes, diffusion, microinjection, virus vectors, calcium phosphate, and particle bombardment. Techniques are well-known to the art for the introduction of DNA into monocots as well as dicots, as are the techniques for culturing such plant tissues and regenerating those tissues.

Many of the procedures useful for practicing the present invention, whether or not described herein in detail, are well known to those skilled in the art of plant molecular biology. Standard techniques for cloning, DNA isolation, amplification and purification, for enzymatic reactions involving DNA ligase, DNA polymerase, restriction endonucleases and the like, and various separation techniques are those known and commonly employed by those skilled in the art. A number of standard techniques are described in Sambrook et al. (1989) Molecular Cloning, Second Edition, Cold Spring Harbor Laboratory, Plainview, N.Y.; Maniatis et al. (1982) Molecular Cloning, Cold Spring Harbor Laboratory, Plainview, N.Y.; Wu (ed.) (1993) Meth. Enzymol. 218, Part I; Wu (ed.) (1979) Meth. Enzymol. 68; Wu et al. (eds.) (1983) Meth. Enzymol. 100 and 101; Grossman and Moldave (eds.) Meth. Enzymol. 65; Glover (ed.) (1985) DNA Cloning Vol. I and II, IRL Press, Oxford, UK; Hames and Higgins (eds.) (1985) Nucleic Acid Hybridization, IRL Press, Oxford, UK; Kaufman (1987) in Genetic Engineering Principles and Methods, J. K. Setlow, ed., Plenum Press, NY, pp. 155-198; Fitchen et al. 1993. Annu. Rev. Microbiol. 47:739-764; Tolstoshev et al. (1993) in Genomic Research in Molecular Medicine and Virology, Academic Press. Abbreviations and nomenclature are standard in the field and commonly used in professional journals as cited herein.

All references and patent documents cited herein reflect the level of skill in the relevant arts and are incorporated by reference in their entireties to the extent there is no inconsistency with the present disclosure.

Where features or aspects of the invention are described in terms of Markush groups or other groupings of alternatives, those skilled in the art recognize that the invention is intended to relate to any individual member or subgroup of members of the Markush group or other group.

TABLE 3 DNA Sequence encoding Herbicide resistant Waterhemp PPX2L (SEQ ID NO: 13), derived from analysis of multiple cloning events ATGGTAATTCAATCCATTACCCACCTTTCACCAAACCTTGCATTGCCATCGCCATTGTCAGTTTCAACCA AGAACTACCCAGTAGCTGTAATGGGCAACATTTCTGAGCGGGAAGAACCCACTTCTGCTAAAAGGGTTGC TGTTGTTGGTGCTGGAGTTAGTGGACTTGCTGCTGCATATAAGCTAAAATCCCATGGTTTGAGTGTGACA TTGTTTGAAGCTGATTCTAGAGCTGGAGGCAAACTTAAAACTGTTAAAAAAGATGGTTTTATTTGGGATG AGGGGGCAAATACTATGACAGAAAGTGAGGCAGAGGTCTCGAGTTTGATCGATGATCTTGGGCTTCGTGA GAAGCAACAGTTGCCAATTTCACAAAATAAAAGATACATAGCTAGAGACGGTCTTCCTGTGCTACTACCT TCAAATCCCGCTGCACTACTCACGAGCAATATCCTTTCAGCAAAATCAAAGCTGCAAATTATGTTGGAAC CATTTCTCTGGAGAAAACACAATGCTACTGAACTTTCTGATGAGCATGTTCAGGAAAGCGTTGGTGAATT TTTTGAGCGACATTTTGGGAAAGAGTTTGTTGATTATGTTATCGACCCTTTTGTTGCGGGTACATGTGGA GATCCTCAATCGCTTTCCATGCACCATACATTTCCAGAAGTATGGAATATTGAAAAAAGGTTTGGCTCTG TGTTTGCTGGACTAATTCAATCAACATTGTTATCTAAGAAGGAAAAGGGTGGAGAAAATGCTTCTATTAA GAAGCCTCGTGTACGTGGTTCATTTTCATTTCAAGGTGGAATGCAGACACTTGTTGACACAATGTGCAAA CAGCTTGGTGAAGATGAACTCAAACTCCAGTGTGAGGTGCTGTCCTTGTCATATAACCAGAAGGGGATCC CCTCATTAGGGAATTGGTCAGTCTCTTCTATGTCAAATAATACCAGTGAAGATCAATCTTATGATGCTGT GGTTGTCACTGCTCCAATTCGCAATGTCAAAGAAATGAAGATTATGAAATTTGGAAATCCATTTTCACTT GACTTTATTCCAGAGGTGACGTACGTACCCCTTTCCGTTATGATTACTGCATTCAAAAAGGATAAAGTGA AGAGACCTCTTGAGGGCTTCGGAGTTCTTATCCCCTCTAAAGAGCAACATAATGGACTGAAGACTCTTGG TACTTTATTTTCCTCCATGATGTTTCCTGATCGTGCTCCATCTGACATGTGTCTCTTTACTACATTTGTC GGAGGAAGCAGAAATAGAAAACTTGCAAACGCTTCAACGGATGAATTGAAGCAAATAGTTTCTTCTGACC TTCAGCAGCTGTTGGGCACTGAGGACGAACCTTCATTTGTCAATCATCTCTTTTGGAGCAACGCATTCCC ATTGTATGGACACAATTACGATTCTGTTTTGAGAGCCATAGACAAGATGGAAAAGGATCTTCCTGGATTT TTTTATGCAGGTAACCATAAGGGTGGACTTTCAGTGGGAAAAGCGATGGCCTCCGGATGCAAGGCTGCGG AACTTGTAATATCCTATCTGGACTCTCATATATATGTGAAGATGGATGAGAAGACCGCGTAA

TABLE 4 Herbicide-resistant PPO2 Protein Sequence (SEQ ID NO: 14), derived from analysis of multiple cloning events. Bolded G corresponds to single glycine residue where sensitive protein has double glycine residue. MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAKRVAVVGAGVSGLAA AYKLKSHGLSVTLFEADSRAGGKLKTVKKDGFIWDEGANTMTESEAEVSSLIDDLGLR EKQQLPISQNKRYIARDGLPVLLPSNPAALLTSNILSAKSKLQIMLEPFLWRKHNATE LSDEHVQESVGEFFERHFGKEFVDYVIDPFVAGTCGDPQSLSMHHTFPEVWNIEKRFG SVFAGLIQSTLLSKKEKGGENASIKKPRVRGSFSFQGGMQTLVDTMCKQLGEDELKLQ CEVLSLSYNQKGIPSLGNWSVSSMSNNTSEDQSYDAVVVTAPIRNVKEMKIMKFGNPF SLDFIPEVTYVPLSVMITAFKKDKVKRPLEGFGVLIPSKEQHNGLKTLGTLFSSMMFP DRAPSDMCLFTTFVGGSRNRKLANASTDELKQIVSSDLQQLLGTEDEPSFVNHLFWSN AFPLYGHNYDSVLRAIDKMEKDLPGFFYAGNHKGGLSVGKAMASGCKAAELVISYLDS HIYVKMDEKTA

TABLE 5 DNA Sequence Encoding Wild type (Herbicide-sensitive) Waterhemp PPO (SEQ ID NO: 15), derived from analysis of multiple cloning events ATGGTAATTCAATCCATTACCCACCTTTCACCAAACCTTGCATTGCCATCGCCATTGTCAGTTTCAACCA AGAACTACCCAGTAGCTGTAATGGGCAACATTTCTGAGCGGGAAGAACCCACTTCTGCTAAAAGGGTTGC TGTTGTTGGTGCTGGAGTTAGTGGACTTGCTGCTGCATATAAGCTAAAATCCCATGGTTTGAGTGTGACA TTGTTTGAAGCTGATTCTAGAGCTGGAGGCAAACTTAAAACTGTTAAAAAAGATGGTTTTATTTGGGATG AGGGGGCAAATACTATGACAGAAAGTGAGGCAGAGGTCTCGAGTTTGATCGATGATCTTGGGCTTCGTGA GAAGCAACAGTTGCCAATTTCACAAAATAAAAGATACATAGCTAGAGACGGTCTTCCTGTGCTACTACCT TCAAATCCCGCTGCACTACTCACGAGCAATATCCTTTCAGCAAAATCAAAGCTGCAAATTATGTTGGAAC CATTTCTCTGGAGAAAACACAATGCTACTGAACTTTCTGATGAGCATGTTCAGGAAAGCGTTGGTGAATT TTTTGAGCGACATTTTGGGAAAGAGTTTGTTGATTATGTTATCGACCCTTTTGTTGCGGGTACATGTGGT GGAGATCCTCAATCGCTTTCCATGCACCATACATTTCCAGAAGTATGGAATATTGAAAAAAGGTTTGGCT CTGTGTTTGCTGGACTAATTCAATCAACATTGTTATCTAAGAAGGAAAAGGGTGGAGAAAATGCTTCTAT TAAGAAGCCTCGTGTACGTGGTTCATTTTCATTTCAAGGTGGAATGCAGACACTTGTTGACACAATGTGC AAACAGCTTGGTGAAGATGAACTCAAACTCCAGTGTGAGGTGCTGTCCTTGTCATATAACCAGAAGGGGA TCCCCTCATTAGGGAATTGGTCAGTCTCTTCTATGTCAAATAATACCAGTGAAGATCAATCTTATGATGC TGTGGTTGTCACTGCTCCAATTCGCAATGTCAAAGAAATGAAGATTATGAAATTTGGAAATCCATTTTCA CTTGACTTTATTCCAGAGGTGACGTACGTACCCCTTTCCGTTATGATTACTGCATTCAAAAAGGATAAAG TGAAGAGACCTCTTGAGGGCTTCGGAGTTCTTATCCCCTCTAAAGAGCAACATAATGGACTGAAGACTCT TGGTACTTTATTTTCCTCCATGATGTTTCCTGATCGTGCTCCATCTGACATGTGTCTCTTTACTACATTT GTCGGAGGAAGCAGAAATAGAAAACTTGCAAACGCTTCAACGGATGAATTGAAGCAAATAGTTTCTTCTG ACCTTCAGCAGCTGTTGGGCACTGAGGACGAACCTTCATTTGTCAATCATCTCTTTTGGAGCAACGCATT CCCATTGTATGGACACAATTACGATTCTGTTTTGAGAGCCATAGACAAGATGGAAAAGGATCTTCCTGGA TTTTTTTATGCAGGTAACCATAAGGGTGGACTTTCAGTGGGAAAAGCGATGGCCTCCGGATGCAAGGCTG CGGAACTTGTAATATCCTATCTGGACTCTCATATATATGTGAAGATGGATGAGAAGACCGCGTAA

TABLE 6 Wild type Waterhemp PPO Amino Acid Sequence (SEQ ID NO: 16), derived from analysis of multiple cloning events MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAKRVAVVGAGVSGLAAAYKLKSHGLSVTLFEAD SRAGGKLKTVKKDGFIWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNPAALLTSN ILSAKSKLQIMLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDPFVAGTCGGDPQSLSMHHTFPEV WNIEKRFGSVFAGLIQSTLLSKKEKGGENASIKKPRVRGSFSFQGGMQTLVDTMCKQLGEDELKLQCEVLSLSYN QKGIPSLGNWSVSSMSNNTSEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEVTYVPLSVMITAFKKDKVK RPLEGFGVLIPSKEQHNGLKTLGTLFSSMMFPDPAPSDMCLFTTFVGGSRNRKLANASTDELKQIVSSDLQQLLG TEDEPSFVNHLFWSNAFPLYGHNYDSVLRAIDKMEKDLPGFFYAGNHKGGLSVGKAMASGCKAAELVISYLDSHI YVKMDEKTA

TABLE 7 Amino acid and cDNA sequences of herbicide-susceptible Amaranthus tuberculatus biotype WC plastid protoporphyrinogen oxidase (PPX1) mRNA, complete cds; nuclear gene for plastid product, corresponding to NCBI ACCESSION DQ386112; SEQ ID NO: 17 (cDNA) and NO: 18 (amino acid) MSAMALSSSILQCPPHSDISFRFFAHTRTQPPIFFGRPRKLSYI HCSTSSSSTANYQNTITSQGEGDKVLDCVIVGAGISGLCIAQALSTKHIQSNLNFIVT EAKHRVGGNITTMESDGYIWEEGPNSFQPSDPVLTMAVDSGLKDDLVLGDPNAPRFVL WNGKLRPVPSKPTDLPFFDLMSFPGKIRAGLGALGLRPPPPSYEESVEEFVRRNLGDE VFERLIEPFCSGVYAGDPAKLSMKAAFGKVWTLEQKGGSIIAGTLKTIQERKNNPPPP RDPRLPKPKGQTVGSFRKGLIMLPTAIAARLGSKVKLSWTLSNIDKSLNGEYNLTYQT PDGPVSVRTKAVVMTVPSYIASSLLRPLSDVAADSLSKFYYPPVAAVSLSYPKEAIRP ECLIDGELKGFGQLHPRSQGVETLGTIYSSSLFPGRAPPGRTLILSYIGGATNLGILQ KSEDELAETVDKDLRKILINPNAKGSRVLGVRVWPKAIPQFLVGHFDVLDAAKAGLAN AGQKGLFLGGNYVSGVALGRCIEGAYDSASEVVDFLSQYKDK 1 atgagtgcga tggcgttatc gagcagcatt ctacaatgtc cgccgcactc cgacatctcg 61 ttccgctttt ttgctcatac acgaacccaa ccccccatct tcttcggaag accacgaaaa 121 ttatcatata tccattgttc cacaagctca agctcaactg ccaattacca gaacaccatt 181 acgagccaag gagaaggaga taaagtatta gattgtgtaa ttgttggagc tggtatcagt 241 ggactttgca ttgctcaggc tctttctacc aaacacattc aatccaatct caatttcatt 301 gtcactgaag ctaaacatcg tgttggaggt aatatcacta ccatggagtc cgatggctat 361 atctgggaag agggtcctaa tagtttccaa ccctccgatc ctgtgcttac tatggcggtt 421 gacagtggat tgaaagacga tttggtcttg ggagatccta atgcccctcg tttcgtgctc 481 tggaatggta aattaaggcc tgttccttcc aaacctacgg accttccctt ttttgatctc 541 atgagctttc ctggtaagat tagggctggt cttggtgcac ttggtcttcg tcctcctcct 601 ccttcttatg aggaatctgt tgaagaattt gtgcgccgta atctcggcga tgaggtcttc 661 gaacgcttga tcgaaccctt ttgttctggt gtctatgctg gtgatcctgc aaagttgagt 721 atgaaagctg catttggaaa ggtctggacc ttagagcaaa agggtggtag tatcatagcc 781 ggtacactca aaactattca ggaaaggaaa aataatcctc caccccctcg agacccccgc 841 cttcctaaac ctaagggcca gactgttgga tcctttagga aagggctcat tatgttacct 901 accgccattg ctgctaggct tggcagtaaa gtcaaactat cgtggacact ttctaatatt 961 gataagtcgc tcaatggaga atacaatctc acttatcaaa cacccgatgg accggtttct 1021 gttaggacca aagcggttgt catgaccgtc ccttcgtaca ttgcaagtag cttgcttcgt 1081 ccgctctcag atgttgctgc agattctctt tctaaatttt actatccacc agtcgcagca 1141 gtgtcccttt cttatcccaa agaagcaatt agaccagaat gcttgatcga tggtgaacta 1201 aaaggattcg ggcaattgca tccccgcagc cagggtgtgg aaaccttggg aacaatttat 1261 agttcatctc ttttccctgg tcgagcaccc cccggtagga ccttgatctt gagctacatt 1321 ggaggtgcta caaatcttgg catattacaa aagagtgaag atgaacttgc ggagacagtt 1381 gataaggatc tcagaaaaat tctgataaat ccaaatgcga aaggcagccg tgttctggga 1441 gtgagagtat ggccaaaagc aatcccccaa tttttagttg gtcactttga tgtgctagat 1501 gctgcaaaag ctggtttggc aaatgctggg caaaaggggt tgtttcttgg tggtaattat 1561 gtatcaggtg ttgccttggg gaggtgtata gagggtgctt atgactctgc ttctgaggta 1621 gtggatttcc tctcacagta caaagataag tag

TABLE 8 Coding and amino acid sequences of Amaranthus tuberculatus biotype herbicide-susceptible WC mitochondrial protoporphyrinogen oxidase (PPX2) mRNA, nuclear gene for mitochondrial product, corresponding to NCBI Accession DQ386113 and SEQ ID NO: 19 (cDNA) and NO: 20 (amino acid) MGNISERDEPTSAKRVAVVGAGVSGLAAAYKLKSHGLNVTLFEA DSRAGGKLKTVKKDGFIWDEGANTMTESEAEVSSLIDDLGLREK QQLPISQNKRYIARDGLPVLLPSNPAALLTSNILSAKSKLQIMLEPF FWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDPFVAGTC GGDPQSLSMHHTFPEVWNIEKRFGSVFAGLIQSTLLSKKEKGGGG NASIKKPRVRGSFSFHGGMQTLVDTICKQLGEDELKLQCEVLSLS YNQKGIPSLGNWSVSSMSNNTSEDQSYDAVVVTAPIRNVKEMKIM KFGNPFSLDFIPEVSYVPLSVMITAFKKDKVKRPLEGFGVLIPSKEQ HNGLKTLGTLFSSMMFPDRAPSDMCLFTTFVGGSRNRKLANASTD ELKQIVSSDLQQLLGTEDEPSFVNHLFWSNAFPLYGHNYDSVLRAI DKMEKDLPGFFYAGNHKGGLSVGKAMASGCKAAELVISYLDSHIY VKMDEKTA 1 atgggcaaca tttctgagcg ggatgaaccc acttctgcta aaagggttgc tgttgttggt 61 gctggagtta gtggacttgc tgctgcatat aagctaaaat cccatggttt gaatgtgaca 121 ttgtttgaag ctgattctag agctggaggc aaacttaaaa ctgttaaaaa agatggtttt 181 atttgggatg agggggcaaa tactatgaca gaaagtgagg cagaagtctc gagtttgatc 241 gatgatcttg ggcttcgtga gaagcaacag ttgccaattt cacaaaataa aagatacata 301 gctagagatg gtcttcctgt gctactacct tcaaatcccg ctgcactgct cacgagcaat 361 atcctttcag caaaatcaaa gctgcaaatt atgttggaac catttttctg gagaaaacac 421 aatgctactg agctttctga tgagcatgtt caggaaagcg ttggtgaatt ttttgagcga 481 cattttggga aagagtttgt tgattatgtt attgaccctt ttgttgcggg tacatgtggt 541 ggagatcctc aatcgctttc tatgcaccat acatttccag aagtatggaa tattgaaaaa 601 aggtttggct ctgtgtttgc tggactaatt caatcaacat tgttatctaa gaaggaaaag 661 ggtggaggag gaaatgcttc tatcaagaag cctcgtgtac gtggttcatt ttcattccat 721 ggtggaatgc agacacttgt tgacacaata tgcaaacagc ttggtgaaga tgaactcaaa 781 ctccagtgtg aggtgctgtc cttgtcatac aaccagaagg ggatcccttc attagggaat 841 tggtcagtct cttctatgtc aaataatacc agtgaagatc aatcttatga tgctgtggtt 901 gtcactgctc caattcgcaa tgtcaaagaa atgaagatta tgaaattcgg aaatccattt 961 tcacttgact ttattccaga ggtgagttac gtacccctct ctgttatgat tactgcattc 1021 aagaaggata aagtgaagag accactcgag ggctttggag ttcttatccc ctctaaagag 1081 caacataatg gactgaagac tcttggtact ttattttcct ccatgatgtt tcccgatcgt 1141 gctccatctg acatgtgtct ctttactaca tttgtcggag gaagcagaaa tagaaaactt 1201 gcaaacgctt caacggatga attgaagcaa atagtttctt ctgaccttca gcagctgttg 1261 ggcactgagg acgaaccttc atttgtcaat catctctttt ggagcaacgc attcccgttg 1321 tatggacaca attacgattc tgttttgaga gccatagaca agatggaaaa ggatcttcct 1381 ggattttttt atgcaggtaa ccataagggt ggactttcag tgggaaaagc gatggcctcc 1441 ggatgcaagg ctgcggaact tgtaatatcc tatctggact ctcatatata tgtgaagatg 1501 gatgagaaga ccgcgtaa

TABLE 9 Coding and amino acid sequence of Amaranthus tuberculatus biotype herbicide-susceptible WC mitochondrial protoporphyrinogen oxidase (PPX2L) mRNA, nuclear gene for mitochondrial product, corresponding to NCBI Accession DQ386114 and SEQ ID NO: 21 (cDNA) and NO: 22 (amino acid) MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAK RVAVVGAGVSGLAAAYKLKSHGLSVTLFEADSRAGGKLKTVKKD GFIWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARDG LPVLLPSNPAALLTSNILSAKSKLQIMLEPFLWRKHNATELSDEHV QESVGEFFERHFGKEFVDYVIDPFVAGTCGGDPQSLSMHHTFPEV WNIEKRFGSVFAGLIQSTLLSKKEKGGENASIKKPRVRGSFSFQGG MQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWSVSSM SNNTSEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEVTYVPL SVMITAFKKDKVKRPLEGFGVLIPSKEQHNGLKTLGTLFSSMMFPD RAPSDMCLFTTFVGGSRNRKLANASTDELKQIVSSDLQQLLGTEDE PSFVNHLFWSNAFPLYGHNYDSVLRAIDKMEKDLPGFFYAGNHKG GLSVGKAMASGCKAAELVISYLDSHIYVKMDEKTA 1 atggtaattc aatccattac ccacctttca ccaaaccttg cattgccatc gccattgtca 61 gtttcaacca agaactaccc agtagctgta atgggcaaca tttctgagcg ggaagaaccc 121 acttctgcta aaagggttgc tgttgttggt gctggagtta gtggacttgc tgctgcatat 181 aagctaaaat cccatggttt gagtgtgaca ttgtttgaag ctgattctag agctggaggc 241 aaacttaaaa ctgttaaaaa agatggtttt atttgggatg agggggcaaa tactatgaca 301 gaaagtgagg cagaggtctc gagtttgatc gatgatcttg ggcttcgtga gaagcaacag 361 ttgccaattt cacaaaataa aagatacata gctagagacg gtcttcctgt gctactacct 421 tcaaatcccg ctgcactact cacgagcaat atcctttcag caaaatcaaa gctgcaaatt 481 atgttggaac catttctctg gagaaaacac aatgctactg aactttctga tgagcatgtt 541 caggaaagcg ttggtgaatt ttttgagcga cattttggga aagagtttgt tgattatgtt 601 atcgaccctt ttgttgcggg tacatgtggt ggagatcctc aatcgctttc catgcaccat 661 acatttccag aagtatggaa tattgaaaaa aggtttggct ctgtgtttgc tggactaatt 721 caatcaacat tgttatctaa gaaggaaaag ggtggagaaa atgcttctat taagaagcct 781 cgtgtacgtg gttcattttc atttcaaggt ggaatgcaga cacttgttga cacaatgtgc 841 aaacagcttg gtgaagatga actcaaactc cagtgtgagg tgctgtcctt gtcatataac 901 cagaagggga tcccctcatt agggaattgg tcagtctctt ctatgtcaaa taataccagt 961 gaagatcaat cttatgatgc tgtggttgtc actgctccaa ttcgcaatgt caaagaaatg 1021 aagattatga aatttggaaa tccattttca cttgacttta ttccagaggt gacgtacgta 1081 cccctttccg ttatgattac tgcattcaaa aaggataaag tgaagagacc tcttgagggc 1141 ttcggagttc ttatcccctc taaagagcaa cataatggac tgaagactct tggtacttta 1201 ttttcctcca tgatgtttcc tgatcgtgct ccatctgaca tgtgtctctt tactacattt 1261 gtcggaggaa gcagaaatag aaaacttgca aacgcttcaa cggatgaatt gaagcaaata 1321 gtttcttctg accttcagca gctgttgggc actgaggacg aaccttcatt tgtcaatcat 1381 ctcttttgga gcaacgcatt cccattgtat ggacacaatt acgattctgt tttgagagcc 1441 atagacaaga tggaaaagga tcttcctgga tttttttatg caggtaacca taagggtgga 1501 ctttcagtgg gaaaagcgat ggcctccgga tgcaaggctg cggaacttgt aatatcctat 1561 ctggactctc atatatacgt gaagatggat gagaagaccg cgtaa //

TABLE 10 Amaranthus tuberculatus biotype herbicide-resistant AC plastid protoporphyrinogen oxidase (PPX1) mRNA, nuclear gene for plastid product, corresponding to NCBI Accession DQ386115 and SEQ ID NO: 23 (cDNA) and NO: 24 (amino acid) MSAMALSSSILQCPPHSDISFRFFAHTRTPSPIFFGRTRKLSYI HCSTSSSSTANYQNTITSQGEGDKVLDCVIVGAGISGLCIAQALS TKHIQSNLNFIVTEAKHRVGGNITTMESDGYIWEEGPNSFQPSDP VLTMAVDSGLKDDLVLGDPNAPRFVLWNGKLRPVPSKPTDLPF FDLMSFPGKIRAGLGALGLRPPPPPPSYEESVEEFVRRNLGDEV FERLIEPFCSGVYAGDPAKLSMKAAFGKVWTLEQKGGSIIAGTL KTIQERKNNPPPPRDPRLPKPKGQTVGSFRKGLIMLPTAIAARLG SKVKLSWTLSNIDKSLNGEYNLTYQTPDGPVSVRTKAVVMTVPSY IASSLLRPLSDVAADSLSKFYYPPVAAVSLSYPKEAIRPECLIDGEL KGFGQLHPRSQGVETLGTIYSSSLFPGRAPPGRTLILSYIGGATNLGI LQKSEDELAETVDKDLRKILINPNAKGSRVLGVRVWPKAIPQFLVG HFDVLDAAKAGLANAGLKGLFLGGNYVSGVALGRCIEGAYDSASE VVDFLSQYKDK 1 atgagtgcga tggcgttatc gagcagcatt ctacaatgtc cgccgcactc cgacatctcg 61 ttccgctttt ttgctcatac acgaacccca tcccccatct tcttcggaag aacacgaaaa 121 ttatcatata tccattgttc cacaagctca agctcaactg ccaattacca gaacacgatt 181 acgagccaag gagaaggaga taaagtatta gattgtgtaa ttgttggagc tggtatcagt 241 ggactttgca ttgctcaggc tctttctacc aaacacattc aatccaatct caatttcatt 301 gtcactgaag ctaaacatcg tgttggaggt aatatcacta ccatggagtc cgatggctat 361 atctgggaag agggtcctaa tagtttccaa ccctccgatc ctgtgcttac tatggcggtt 421 gacagtggat tgaaagacga tttagtcttg ggagatccta atgcccctcg tttcgtgctc 481 tggaatggta aattaaggcc tgttccttcc aaacctacgg accttccctt ttttgatctc 541 atgagctttc ctggtaagat tagggctggt cttggtgcac ttggtcttcg tcctcctcct 601 cctcctcctt cttatgagga atctgttgaa gaatttgtgc gccgtaatct cggcgatgag 661 gtcttcgaac gcttgatcga acccttttgt tctggtgtct atgctggtga tcctgcaaag 721 ttgagtatga aagctgcatt tggaaaggtc tggaccttag agcaaaaggg tggtagtatc 781 atagccggta cactcaaaac tattcaggaa aggaaaaata atcctccacc ccctcgagac 841 ccccgccttc ctaaacctaa gggccagact gttggatcct ttaggaaagg gctcattatg 901 ttacctaccg ccattgctgc taggcttggc agtaaagtca aactatcgtg gacactttct 961 aatattgata agtcgctcaa tggagaatac aatctcactt atcaaacacc cgatggaccg 1021 gtttctgtta ggaccaaagc ggttgtcatg accgtccctt cgtacattgc aagtagcttg 1081 cttcgtccgc tctcagatgt tgctgcagat tctctttcta aattttacta tccaccagtc 1141 gcagcagtgt ccctttctta tcccaaagaa gcaattagac cagaatgctt gattgatgga 1201 gaactaaaag gattcgggca attgcatccc cgcagccagg gtgtggaaac cttgggaaca 1261 atttatagtt catctctttt ccctggtcga gcaccacccg gtaggacctt gatcttgagc 1321 tacattggag gtgctacaaa tcttggcata ttacaaaaga gtgaagatga actcgcggag 1381 acagttgata aggatctcag aaaaattctg ataaatccaa atgcgaaagg cagccgtgtt 1441 ctgggagtga gagtatggcc aaaggcaatc ccccaatttt tagttggtca ctttgatgtg 1501 ctagatgctg caaaagctgg tttggcaaat gctgggctaa aggggttgtt tcttggtggt 1561 aattatgtat caggtgttgc cttggggagg tgtatagagg gtgcttatga ctctgcttct 1621 gaggtagtgg atttcctctc acagtacaaa gataagtag //

TABLE 11 Amaranthus tuberculatus biotype herbicide-resistant AC mitochondrial protoporphyrinogen oxidase (PPX2L) mRNA, complete cds; nuclear gene for mitochondrial product, corresponding to NCBI Accession DQ386116 and to SEQ ID NO: 25 (cDNA) and NO: 26 (amino acid) MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAK RVAVVGAGVSGLAAAYKLKSHGLSVTLFEADSRAGGKLKTVKK DGFIWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIAR DGLPVLLPSNPAALLTSNILSAKSKLQIMLEPFLWRKHNATELSDE HVQESVGEFFERHFGKEFVDYVIDPFVAGTCGDPQSLSMHHTF PEVWNIEKRFGSVFAGLIQSTLLSKKEKGGENASIKKPRVRGSFS FQGGMQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWS VSSMSNNTSEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEV TYVPLSVMITAFKKDKVKRPLEGFGVLIPSKEQHNGLKTLGTLFSS MMFPDRAPSDMCLFTTFVGGSRNRKLANASTDELKQIVSSDLQQLL GTEDEPSFVNHLFWSNAFPLYGHNYDCVLRAIDKMEKDLPGFFYA GNHKGGLSVGKAMASGCKAAELVISYLDSHIYVKMDEKTA 1 atggtaattc aatccattac ccacctttca ccaaaccttg cattgccatc gccattgtca 61 gtttccacca agaactaccc agtagctgta atgggcaaca tttctgagcg agaagaaccc 121 acttctgcta aaagggttgc tgttgttggt gctggagtta gtggacttgc tgctgcatat 181 aagctaaaat cccatggttt gagtgtgaca ttgtttgaag ctgattctag agctggaggc 241 aaacttaaaa ctgttaaaaa agatggtttt atttgggatg agggggcaaa tactatgaca 301 gaaagtgagg cagaggtctc gagtttgatc gatgatcttg ggcttcgtga gaagcaacag 361 ttgccaattt cacaaaataa aagatacata gctagagacg gtcttcctgt gctactacct 421 tcaaatcccg ctgcactact cacgagcaat atcctttcag caaaatcaaa gctgcaaatt 481 atgttggaac catttctctg gagaaaacac aatgctactg aactttctga tgagcatgtt 541 caggaaagcg ttggtgaatt ttttgagcga cattttggga aagagtttgt tgattatgtt 601 attgaccctt ttgttgcggg tacatgtgga gatcctcaat cgctttccat gcaccataca 661 tttccagaag tatggaatat tgaaaaaagg tttggctctg tgtttgctgg actaattcaa 721 tcaacattgt tatctaagaa ggaaaagggt ggagaaaatg cttctattaa gaagcctcgt 781 gtacgtggtt cattttcatt tcaaggtgga atgcagacac ttgttgacac aatgtgcaaa 841 cagcttggtg aagatgaact caaactccag tgtgaggtgc tgtccttgtc atataaccag 901 aaggggatcc cctcattagg gaattggtca gtctcttcta tgtcaaataa taccagtgaa 961 gatcaatctt atgatgctgt ggttgtcact gctccaattc gcaatgtcaa agaaatgaag 1021 attatgaaat ttggaaatcc attttcactt gactttattc cagaggtgac gtacgtaccc 1081 ctttccgtta tgattactgc attcaaaaag gataaagtga agagacctct tgagggcttc 1141 ggagttctta tcccctctaa agagcaacat aatggactga agactcttgg tactttattt 1201 tcctccatga tgtttcctga tcgtgctcca tctgacatgt gtctctttac tacatttgtc 1261 ggaggaagca gaaatagaaa acttgcaaac gcttcaacgg atgaattgaa gcaaatagtt 1321 tcttctgacc ttcagcagct gttgggcact gaggacgaac cttcatttgt caatcatctc 1381 ttttggagca acgcattccc attgtatgga cacaattacg attgtgtttt gagagccata 1441 gacaagatgg aaaaggatct tcctggattt ttttatgcag gtaaccataa gggtggactt 1501 tcagtgggaa aagcgatggc ctccggatgc aaggctgcgg aacttgtaat atcctatctg 1561 gactctcata tatacgtgaa gatggatgag aagaccgcgt aa //

TABLE 12 Amaranthus tuberculatus biotype herbicide-susceptible AC mitochondrial protoporphyrinogen oxidase (PPX2L) mRNA, nuclear gene for mitochondrial product, corresponding to NCBI Accession DQ386117 and to SEQ ID NO: 27 and NO: 28 MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAK RVAVVGAGVSGLAAAYKLKSHGLSVTLFEADSRAGGKLKTVKKDGFIWDEG ANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARAGLPVLLPSNPAALLTS NILSAKSKLQIMLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVID PFVAGTCGGDPQSLSMHHTFPEVWNIEKRFGSVFAGLIQSTLLSKKEKGG ENASIKKPRVRGSFSFQGGMQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIP SLGNWSVSSMSNNTSEDQSYDAVVVTAPIRNVKEMKIMKFGNPFSLDFIPEV TYVPLSVMITAFKKDKVKRPLEGFGVLIPSKEQHNGLKTLGTLFSSMMFPDR APSDMCLFTTFVGGSRNRKLANASTDELKQIVSSDLQQLLGTEDEPSFVNH LFWSNAFPLYGHNYDSVLRAIDKMEKDLPGFFYAGNHKGGLSVGKAMASGC KAAELVISYLDSHIYVKMDEKTA 1 atggtaattc aatccattac ccacctttca ccaaaccttg cattgccatc gccattgtca 61 gtttcaacca agaactaccc agtagctgta atgggcaaca tttctgagcg ggaagaaccc 121 acttctgcta aaagggttgc tgttgttggt gctggagtta gtggacttgc tgctgcatat 181 aagctaaaat cccatggttt gagtgtgaca ttgtttgaag ctgattctag agctggaggc 241 aaacttaaaa ctgttaaaaa agatggtttt atttgggatg agggggcaaa tactatgaca 301 gaaagtgagg cagaggtctc gagtttgatc gatgatcttg ggcttcgtga gaagcaacag 361 ttgccaattt cacaaaataa aagatacata gctagagccg gtcttcctgt gctactacct 421 tcaaatcccg ctgcactact cacgagcaat atcctttcag caaaatcaaa gctgcaaatt 481 atgttggaac catttctctg gagaaaacac aatgctactg aactttctga tgagcatgtt 541 caggaaagcg ttggtgaatt ttttgagcga cattttggga aagagtttgt tgattatgtt 601 attgaccctt ttgttgcggg tacatgtggt ggagatcctc aatcgctttc catgcaccat 661 acatttccag aagtatggaa tattgaaaaa aggtttggct ctgtgtttgc cggactaatt 721 caatcaacat tgttatctaa gaaggaaaag ggtggagaaa atgcttctat taagaagcct 781 cgtgtacgtg gttcattttc atttcaaggt ggaatgcaga cacttgttga cacaatgtgc 841 aaacagcttg gtgaagatga actcaaactc cagtgtgagg tgctgtcctt gtcatataac 901 cagaagggga tcccctcact agggaattgg tcagtctctt ctatgtcaaa taataccagt 961 gaagatcaat cttatgatgc tgtggttgtc actgctccaa ttcgcaatgt caaagaaatg 1021 aagattatga aatttggaaa tccattttca cttgacttta ttccagaggt gacgtacgta 1081 cccctttccg ttatgattac tgcattcaaa aaggataaag tgaagagacc tcttgagggc 1141 ttcggagttc ttatcccctc taaagagcaa cataatggac tgaagactct tggtacttta 1201 ttttcctcca tgatgtttcc tgatcgtgct ccatctgaca tgtgtctctt tactacattt 1261 gtcggaggaa gcagaaatag aaaacttgca aacgcttcaa cggatgaatt gaagcaaata 1321 gtttcttctg accttcagca gctgttgggc actgaggacg aaccttcatt tgtcaatcat 1381 ctcttttgga gcaacgcatt cccattgtat ggacacaatt acgattctgt tttgagagcc 1441 atagacaaga tggaaaagga tcttcctgga tttttttatg caggtaacca taagggtgga 1501 ctttcagtgg gaaaagcgat ggcctccgga tgcaaggctg cggaacttgt aatatcctat 1561 ctggactctc atatatacgt gaagatggat gagaagaccg cgtaa //

TABLE 13 Amaranthus tuberculatus biotype herbicide-resistant CC mitochondrial protoporphyrinogen oxidase (PPX2L) mRNA, nuclear gene for mitochondrial product, corresponding to Accession DQ386118 and SEQ ID NO: 29 and NO: 30. MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAK RVAVVGAGVSGLAAAYKLKSHGLSVTLFEANSRAGGKLKTVKKDGFIWDEGANTMTES EAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNPAALLTSNILSAKSKLQI MLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDPFVAGTCGDPQSLSMY HTFPEVWNIEKRFGSVFAGLIQSTLLSKKEKGGENASIKKPRVRGSFSFQGGMQTLVD TMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWSVSSMSNNTSEDQSYDAVVVTAPIR NVKEMKIMKFGNPFSLDFIPEVTYVPLSVMITAFKKDKVKRPLEGFGVLIPSKEQHNG LKTLGTLFSSMMFPDRAPSDMCLFTTFVGGSRNRKLANASTDELKQIVSSDLQQLLGT EDEPSFVNHLFWSNAFPLYGHNYDSVLRAIDKMEKDLPGFFYAGNHKGGLSVGKAMAS GCKAAELVISYLDSHIYVKMDEKTA 1 atggtaattc aatccattac ccacctttca ccaaaccttg cattgccatc gccattgtca 61 gtttccacca agaactaccc agtagctgta atgggcaaca tttctgagcg ggaagaaccc 121 acttctgcta aaagggttgc tgttgttggt gctggagtta gtggacttgc tgctgcatat 181 aagctaaaat cccatggttt gagtgtgaca ttgtttgaag ctaattctag agctggaggc 241 aaacttaaaa ctgttaaaaa agatggtttt atttgggatg agggggcaaa tactatgaca 301 gaaagtgagg cagaggtctc gagtttgatc gatgatcttg ggcttcgtga gaagcaacag 361 ttgccaattt cacaaaataa aagatacata gctagagacg gtcttcctgt gctactacct 421 tcaaatcccg ctgcactact cacgagcaat atcctttcag caaaatcaaa gctgcaaatt 481 atgttggaac catttctctg gagaaaacac aatgctactg aactttctga tgagcatgtt 541 caggaaagcg ttggtgaatt ttttgagcga cattttggga aagagtttgt tgattatgtt 601 attgaccctt ttgttgcggg tacatgtgga gatcctcaat cgctttccat gtaccataca 661 tttccagaag tatggaatat tgaaaaaagg tttggctctg tgtttgctgg actaattcaa 721 tcaacattgt tatctaagaa ggaaaagggt ggagaaaatg cttctattaa gaagcctcgt 781 gtacgtggtt cattttcatt tcaaggtgga atgcagacac ttgttgacac aatgtgcaaa 841 cagcttggtg aagatgaact caaactccag tgtgaggtgc tgtccttgtc atataaccag 901 aaggggatcc cctcattagg gaattggtca gtctcttcta tgtcaaataa taccagtgaa 961 gatcaatctt atgatgctgt ggttgtcact gctccaattc gcaatgtcaa agaaatgaag 1021 attatgaaat ttggaaatcc attttcactt gactttattc cagaggtgac gtacgtaccc 1081 ctttccgtta tgattactgc attcaaaaag gataaagtga agagacctct tgagggcttc 1141 ggagttctta tcccctctaa agagcaacat aatggactga agactcttgg tactttattt 1201 tcctccatga tgtttcctga tcgtgctcca tctgacatgt gtctctttac tacatttgtc 1261 ggaggaagca gaaatagaaa acttgcaaac gcttcaacgg atgaattgaa gcaaatagtt 1321 tcttctgacc ttcagcagct gttgggcact gaggacgaac cttcatttgt caatcatctc 1381 ttttggagca acgcattccc attgtatgga cacaattacg attctgtttt gagagccata 1441 gacaagatgg aaaaggatct tcctggattt ttttatgcag gtaaccataa gggtggactt 1501 tcagtgggaa aagcgatggc ctccggatgc aaggctgcgg aacttgtaat atcctatctg 1561 gactctcata tatacgtgaa gatggatgag aagaccgcgt aa //

TABLE 14 Amaranthus tuberculatus biotype WCS (herbicide sensitive) mitochondrial protoporphyrinogen oxidase long form (PPX2L) gene, partial cds from genomic DNA; nuclear gene for mitochondrial product, corresponding to Accesssion DQ394875 and to SEQ ID NO: 31 and NO: 32. The protein coding region begins at 65 and continues beyond 4797, with coding sequence splicing as follows: join(<65 . . . 185, 287 . . . 326, 516 . . . 651, 755 . . . 820, 1227 . . . 1277, 1399 . . . 1455, 2081 . . . 2157, 2646 . . . 2682, 2777 . . . 2842, 3374 . . . >3414) MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAK RVAVVGAGVSGLAAAYKLKSHGLSVTLFEADSRAGGKLKTVKKDGFIWDEGANTMTES EAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNPAALLTSNILSAKSKLQI MLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDPFVAGTCGGDPQSLSM HHTFPEVWNIEK 1 aagaattgaa ttggcagatt gagacaaaat tggattcaga atttagcaaa tttaaaccga 61 tcgtatggta attcaatcca ttacccacct ttcaccaaac cttgcattgc catcgccatt 121 gtcagtttca accaagaact acccagtagc tgtaatgggc aacatttctg agcgggaaga 181 acccagtaag tcaacctttc ttcacatatc ttaaagcaat cccttttcaa ctacactttc 241 ttttgatgat ttcacattct gagttttttt tattggggat ttttagcttc tgctaaaagg 301 gttgctgttg ttggtgctgg agttaggtaa attttatgtt tcttttccag aaagattgta 361 aaattttgct ttgattgttc tgaattttga tgggtttttg cataatgatt tgtatttggg 421 atgggcaaat ttttcagtag atcatactac ttttaacttc tattttctgt ataattttat 481 tgatttccta aactgttttt gtggaattgt tctagtggac ttgctgctgc atataagcta 541 aaatcccatg gtttaagtgt gacattgttt gaagctgatt ctagagctgg aggcaaactt 601 aaaactgtta aaaaagatgg ttttatttgg gatgaggggg caaatactat ggtaatgttt 661 atcaacaatg ctggttttct gatttagaac caattacttg ctggattttg ggtcaattct 721 gtggttaaca tgtcactttc tgatatgctt gtagacagaa agtgaggcag aggtctcgag 781 tttgatcgat gatcttgggc ttcgtgagaa gcaacagttg gtaagttttc tgtctaagcc 841 cattcccttt gcttgctaga gtccgtagcg caaaaatacg gtaatagtca tgatcgtggt 901 aatgacatgg tgatgcggtg acaggagtca tgtgatcgtt attccaacta taggtcaaaa 961 acatgatatt ttccttgtga cgccccaaaa tgcagtattt ttacaccttt acattgcggg 1021 gaaaaatagg tttattatgt tgaaaacctt tacaaggcgg ctgatgcgat gcggccttgt 1081 ttttgcatta tgttcttgaa gcaacttatt atatctttga ttaatgtatc atcagcttaa 1141 aacagcctta ttgtacttct taatctagtt ttgacttttg aggttgcttt tacaagatct 1201 ttatatgatt ggttcttctg tcacagccaa tttcacaaaa taaaagatac atagctagag 1261 acggtcttcc tgtgctagta agtcctctgc atttactttt gacctctatg aacttctaac 1321 actggatact aagttgtatt cgaggcaaat tctgtatttt ccaatctgct tattgacagt 1381 tgcttgcaaa ctttgcagct accttcaaat cccgctgcac tactcacgag caatatcctt 1441 tcagcaaaat caaaggttat caatgctaaa atcatgtttg gtatttgatt acttagcttt 1501 tggtgtatgc aataatttgg tttctaaaac taagtgattg acggaaaagg agggacgaag 1561 gacatagaat tgcaattttg tgttcttcat gtatttttac ttttagagta ggtaagtcac 1621 tttcggtccg tttggttaat ggtactagtt ggtggtaata ggaatgattt gtagtgtaaa 1681 ttttcaagat atatatcatg tcattcccat ggtaatgaaa gtttgatcat aaaaaggttt 1741 tttgttcaca attttccatt accacctaat accacatgtt taaatggtaa tgcattggaa 1801 tgagttttgt gaagaaaatg agtttgttga gaaagaataa gcatggtcat taaatttgtc 1861 aagagatatt cctatcaaaa ttacactagc tttccattat catttcacca tttagtaccg 1921 attaccaaat gggccgttta tagtttggga agagcatacg tttgtgtaaa acttttattt 1981 tgaagttgaa agaatttgtt gcaccttttg ttatgattag gttttgatgt ttttagctgc 2041 aataaatttg ttgatgaaaa agccactact tttttctcag ctgcaaatta tgttggaacc 2101 atttctctgg agaaaacaca atgctactga actttctgat gagcatgttc aggaaaggca 2161 agtgccacat actattaagt gttagttgct gagaatatat ttgaatctaa gatgcacgaa 2221 gaccactggt gcccttgctc tatcaattct gatggaaagg attatcgctg aatttacctt 2281 ctactaaaac atcgataaaa tacttcatta ttagcatcaa aagattccct ccatccttct 2341 ggttttgcta gacttgcctt atgaaggtgt tcaaggagta gtttgctacc cttcaagata 2401 gggtagtggt tgccgtctct cataatttca gtcactcgtt ttcctctcct aattcaagcc 2461 ataattttta tggttcctcc acacaacact tgctaaattt gaaaagtagc aaagaggaag 2521 tgagcaaaat cagcaggagt aggactgatg agtaagagct tgattaagtg tagaggattt 2581 tcttttgtgt tgaatatgaa tgcatcatgc atgactgtag aattgacata atgatttgtc 2641 tgcagcgttg gtgaattttt tgagcgacat tttgggaaag aggtattgtt gccaattgcc 2701 atgctctatt cattccggtg aattaacaaa tgttgtgctt ctgcttacta ttgcttataa 2761 ttattgtttg ttgcagtttg ttgattatgt tattgaccct tttgttgcgg gtacatgtgg 2821 tggagatcct caatcgcttt ccgtgagtta aatactgtgc ttgctttttt ttttcaacat 2881 tttctggagg ctgtaaataa attatactcc ttcctattct aatcaaatat cctatttccc 2941 cttttggcat attcaaattt agttaaatat tgtgtaaatt atttacacaa ttgccattaa 3001 attttcactt ttcccttact cactcttctc atgtgtccct tccccctttt cttaaaattg 3061 gtgcattatc aaataggaca tttgatttga ataggcggga gtttccaatt gtgcttccaa 3121 aggtagcttg tcactttttc tttttcttta aattttgtac catgccatgc attttgaacc 3181 tcaactcatt tcgccataaa ggaatattat gtttgagaag aacgaggata ctattatctt 3241 atagataaca tataggtttc attatcaatg attgtttgat tttcaactct tcttttcctt 3301 tcatgctcat attgatgtta tttctatttg ttatgaatta tgtccattgt gttaatgtct 3361 ttctttattg tagatgcacc atacatttcc agaagtatgg aatattgaaa aaaggtatga 3421 accttaaagc tttaattttc ttcgaactta atgtttctta attgattctt ttggatcaat 3481 ttccataaga atggaaattt aaaaaaaggt atgaacctta aagatttctt cgaacttata 3541 tgttttgtaa ttcatgcttt tagatgttgc accattttat ctatgtgtct taagtttgtt 3601 gtaatcattt gtagaccaaa agaatgaatg gtctggtttg aaatggttca tcgtgcaaaa 3661 atgcgatttt gcttgtgatt gaggtaacat tcaaggtgat gtgtttgtcg tactgtcaaa 3721 tgtcttccta taccatatga tatatatata agcctaaaat gatatattgt atacctttag 3781 gatgtggata gcaggggttc agtacatatg aaaaatcctt gcaatttgat ctgtacgata 3841 caatgtgatt ttgccttttg ccttttgcct tttgttatat gatgatgatt ccatgtgaaa 3901 ttttgggatt tagaaaattc acttgtttaa gaacatttga atcaaacttt caccaatttc 3961 aaccacattt aattgcggca aagccgaact ttaaaagtca ctcccaatct ttgagatatc 4021 caaactccaa aacttctatt agctttcatg ttttcactaa gtaaagttgg tgcgactcct 4081 taccattttc tttattatgc atttcgttga tgtataatag tatagattgg tgctctcttc 4141 gctctccttc caacatgcat aacttctagt tcttgtcgtt ttcttttcct ccctattttt 4201 atttgacttg tagctatttt tgttcactct tctcgcccaa tccaaaactt gtagctaaag 4261 aaacttgatt tcattgattt tgtaactgat atgcaattca tttttgtttg cttttagttg 4321 ttgattcaaa aacaataatg ctaaagccct aatcctaaca tgtcgggtta gctgttgaaa 4381 caatacttga aattgctata aaaagggatt tttttcgggt acttcagttg ttgagattga 4441 tatggtcaag tataatttgt tttaacacaa tttgtaatga tttaatggct tagtttcata 4501 gctgtttgta ttaataaagg aaggaggact atccgaaatt gcaataggaa agagatttta 4561 gttcggtatt tggttgttta aattgatatg gccaagtaat gttcatttta cacaattggt 4621 aatgttttat tggctcaata gtgtttgtaa gtatgcgact caaatttaat caagtataac 4681 ttattgaaac ataaataaat atccattagg tttggctctg tgtttgctgg actaattcaa 4741 tcaacattgt tatctaagaa ggaaaagggt ggagaaaatg cttcataaga agcctcg

TABLE 15 Amaranthus tuberculatus biotype ACR mitochondrial protoporphyrinogen oxidase long form (PPX2L) gene with partial cds; nuclear gene for mitochondrial product, corresponding to NCBI Accession DQ394876 and SEQ ID NO: 33 (DNA) and NO: 34 (amino acid). Splicing is as follows for mRNA: join(<65 . . . 185, 287 . . . 326, 516 . . . 651, 755 . . . 820, 1227 . . . 1277, 1399 . . . 1455, 2080 . . . 2156, 2645 . . . 2681, 2776 . . . 2838, 3366 . . . >3406) CDS join(65 . . . 185, 287 . . . 326, 516 . . . 651, 755 . . . 820, 1227 . . . 1277, 1399 . . . 1455, 2080 . . . 2156, 2645 . . . 2681, 2776 . . . 2838, 3366 . . . >3406) MVIQSITHLSPNLALPSPLSVSTKNYPVAVMGNISEREEPTSAK RVAVVGAGVSGLAAAYKLKSHGLSVTLFEADSRAGGKLKTVKKDGFIWDEGANTMTES EAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNPAALLTSNILSAKSKLQI MLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDPFVAGTCGDPQSLSMH HTFPEVWNIEK 1 aagaattgaa ttggcagatt gagacaaaat tggattcaga atttagcaaa tttaaaccga 61 tcgtatggta attcaatcca ttacccacct ttcaccaaac cttgcattgc catcgccatt 121 gtcagtttcc accaagaact acccagtagc tgtaatgggc aacatttctg agcgagaaga 181 acccagtaag tcaacctttc ttcacatatc ttaaagcaat cccttttcaa ctacactttc 241 ttttgatgat ttcacattct gagttttttt tattggggat ttttagcttc tgctaaaagg 301 gttgctgttg ttggtgctgg agttaggtaa attttatgtt tcttttccag aaagattgta 361 aaattttgct ttgattgttc tgaattttga tgggtttttg cataatgatt tgtatttggg 421 atgggcaaat ttttcagtag atcatactac ttttaacttc tattttctgt ataattttat 481 tgatttccta aattgttttt gtggaattgt tctagtggac ttgctgctgc atataagcta 541 aaatcccatg gtttgagtgt gacattgttt gaagctgatt ctagagctgg aggcaaactt 601 aaaactgtta aaaaagatgg ttttatttgg gatgaggggg caaatactat ggtaatgttt 661 atcaacaatg ctggttttct gatttagaac caattacttg ctggattttg ggtcaattct 721 gtggttaaca tgtcactttc tgatatgctt gtagacagaa agtgaggcag aggtctcgag 781 tttgatcgat gatcttgggc ttcgtgagaa gcaacagttg gtaagttttc tgtctaagcc 841 cattcccttt gcttgctaga gtccgtagcg caaaaatacg gtaatagtca tgatcgtggt 901 aatgacatgg tgatgcggtg acaggagtca tgtgatcgtt attccaacta taggtcaaaa 961 acatgatatt ttccttgtga cgccccaaaa tgcggtattt ttacaccttt acattgcggg 1021 gaaaaatagg tttattatgt tgaaaacctt tacaaggcgg ctgatgcgat gcggccttgt 1081 ttttgcatta tgttctagaa gcaacttatt atatctttga ttaatgtatc atcagcttaa 1141 aacagcctta ttgtacttct taatctagtt ttgacttttg aggttgcttt tacaagatct 1201 ttatatgatt ggttcttctg tcacagccaa tttcacaaaa taaaagatac atagctagag 1261 acggtcttcc tgtgctagta agtcctctgc atttactttt gacctctatg aacttctaac 1321 actggatact aagttgtatt cgaggcaaat tctgtatttt ccaatctgct tattgacagt 1381 tgcttgcata ctttgcagct accttcaaat cccgctgcac tactcacgag caatatcctt 1441 tcagcaaaat caaaggttat caatgctaaa atcatgtttg gtatttgatt acttagcttt 1501 tggtgtatgc aataatttgg tttctaaaac taagtgattg acggaaaagg agggacgaag 1561 gacatagaat tgcaattttg tgttcttcat gtatttttac ttttagagta ggtaagtcac 1621 tttcggtccg tttggttaat ggtactagtt ggtggtaata ggaatgattt gtagtgtaaa 1681 ttttcaagat atatatcatg tcattcccat ggtaatgaaa gtttgatcat aaaaaggttt 1741 tttgttcaca attttccatt accacctaat accacatgtt taaatggtaa tgcattggaa 1801 tgagttttgt gaagaaaatg agtttgttga gaaagaataa gcatggtcat taaatttgtc 1861 aagagatatt cctatcaaaa ttacactagc tttccattat catttcacca tttagtaccg 1921 attaccaaat gggccgttta tagtttggga agagcatacg tttgtgtaaa acttttattt 1981 tgaagttgaa agaatttgtt gcaccttttg ttatgattaa gttttgatgt ttttagctgc 2041 aataatttgt tgatgaaaaa gccactactt ttttctcagc tgcaaattat gttggaacca 2101 tttctctgga gaaaacacaa tgctactgaa ctttctgatg agcatgttca ggaaaggcaa 2161 gtgccacata ctattaagtg ttagttgctg agaatatatt tgaatctaag atgcacgaag 2221 accactggtg cccttgctct atcaattctg atggaaagga ttatcgctga atttaccttc 2281 tactaaaaca tcgataaaat acttcattat tagcatcaaa agattccctc catccttctg 2341 gttttgctag acttgcctta tgaaggtgtt caaggagtag tttgctaccc ttcaagatag 2401 ggtagtggtt gccgtctctc ataatttcag tcactcgttt tcctctccta attcaagcca 2461 taatttttat ggttcctcca cacaacactt gctaaatttg aaaagtagca aagaggaagt 2521 gagcaaaatc agcaggagta ggactgatga gtaagagctt gattaagtgt agaggatttt 2581 cttttgtgtt gaatatgaat gcatcatgca tgactgtaga attgacataa tgatttgtct 2641 gcagcgttgg tgaatttttt gagcgacatt ttgggaaaga ggtattgttg ccaattgcca 2701 tgctctattc attccggtga attaacaaat gttgtgcttc tgcttactat tgcttataat 2761 tattgtttgt tgcagtttgt tgattatgtt attgaccctt ttgttgcggg tacatgtgga 2821 gatcctcaat cgctttccgt gagttaaata ctgtgcttgc tttttttttt caacattttc 2881 tggaggctgt aaataaatta tactccttcc tattctaatc aaatatccta tttccccttt 2941 tggcatattc aaatttagtt aaatattgtg taaattattt acacaattgc cattaaattt 3001 tcacttttcc cttactcttc tcatgtgtcc cttccccctt ttcttaaaat tggtgcatta 3061 tcaaatagga catttgattt gaataggcgg gagtttccaa ttgtgcttcc aaaggtagct 3121 tgtcactttt tctttttctt taaattttgt accatgccat gcattttgaa cctcaactca 3181 tttcgccata aaggaatatt atgtttgaga agaacgagga tactattatc ttatagataa 3241 catataggtt tcattatcaa tgattgtttg attttcaact cttcttttcc tttcatgctc 3301 atattgatgt tatttctatt tgttatgaat tatgtccatt gtgttaatgt ctttctttat 3361 tgtagatgca ccatacattt ccagaagtat ggaatattga aaaaaggtat gaaccttaaa 3421 gctttaattt tcttcgaact taatgtttct taattgattc ttttggatca atttccataa 3481 gaatggaaat ttaaaaaagg gtatgaacct taaagatttc ttcgaactta tatgttttgt 3541 aattcatgct tttagatgct gcaccatttt atctatgtgt cttaagtttg ttgtaatcat 3601 ttgtagacca aaagaatgaa tggtctggtt tgaaatggtt catcgtgcaa aaatgcgatt 3661 ttgcttgtga ttgaggtaac attcaaggtg gtgtgtttgt cgtactgtca aatgtcttcc 3721 tataccatgt gatatatata agcctaaaat gatatattgt acacctttag gatgtggata 3781 gcaggggttc agtacatatg aaaaatcctt gcaatttgat ctgtacgatc aatgtgattt 3841 tgccttttgc cttttgcctt ttgttatatg atgatgattc catgtgaaat tttgggattt 3901 agaaaattca cttgtttaag aacatttgaa tcaaactttc accaatttca accacattta 3961 attgcggcaa agccgaactt taaaagtcac tcccaatctt tgagatatcc aaactccaaa 4021 acttctatta gctttcatgt tttcactaag taaagttggt gcgactcctt accattttct 4081 ttattatgca tttcgttgat gtataatagt atagattggt gctctcttcg ctctccttcc 4141 aacatgcata acttctagtt cttgtcgttt tcttttcctc cctattttta tttgacttgt 4201 agctattttt gttcactctt ctcgcccaat ccatagctaa agaaacttga tttcattgat 4261 tttgtaactg atatgcaatt catttttgtt tgcttttagt tgttgattca aaaacaataa 4321 tgctaaagcc ctaatcctaa catgtcgggt tagctgttga aacaatactt gaaattgcta 4381 taaaaaggga tttttttcgg gtacttcagt tgttgagatt gatatggtca agtataattt 4441 gttttaacac aatttgtaat gatttaatgg cttagtttca tagctgtttg tattaataaa 4501 ggaaggagga ctatctgaaa ttgcaatagg aaagagattt tagttcggta tttggttgtt 4561 taaattgata tggccaagta atgttcattt tacacaattg gtaatgtttt attggctcaa 4621 tagtgtttgt aagtatgcga ctcaaattta atcaagtata acttattgaa acataaataa 4681 atatccatta ggtttggctc tgtgtttgct ggactaattc aatcaacatt gttatctaag 4741 aaggaaaagg gtggagaaaa tgcttcataa gaagcctcgg acgtc

TABLE 16 Coding Squence of Chimeric Herbicide resistant PPXL2 Used in Arabidopsis Transformation Experiments (MTX_SRS; SEQ ID NO: 45; encodes protein of SEQ ID NO: 14 which is identical to SEQ ID NO: 46) ATGGTAATTCAATCCATTACCCACCTTTCACCAAACCTTGCATTGCCATCGCCATTGTCAGTTTCA ACCAAGAACTACCCAGTAGCTGTAATGGGCAACATTTCTGAGCGGGAAGAACCCACTTCTGCTAA AAGGGTTGCTGTTGTTGGTGCTGGAGTTAGTGGACTTGCTGCTGCATATAAGCTAAAATCCCATG GTTTGAGTGTGACATTGTTTGAAGCTGATTCTAGAGCTGGAGGCAAACTTAAAACTGTTAAAAAAG ATGGTTTTATTTGGGATGAGGGGGCAAATACTATGACAGAAAGTGAGGCAGAGGTCTCGAGTTTG ATCGATGATCTTGGGCTTCGTGAGAAGCAACAGTTGCCAATTTCACAAAATAAAAGATACATAGCT AGAGACGGTCTTCCTGTGCTACTACCTTCAAATCCCGCTGCACTACTCACGAGCAATATCCTTTCA GCAAAATCAAAGCTGCAAATTATGTTGGAACCATTTCTCTGGAGAAAACACAATGCTACTGAACTT TCTGATGAGCATGTTCAGGAAAGCGTTGGTGAATTTTTTGAGCGACATTTTGGGAAAGAGTTTGTT GATTATGTTATTGACCCTTTTGTTGCGGGTACATGTGGAGATCCTCAATCGCTTTCCATGCACCAT ACATTTCCAGAAGTATGGAATATTGAAAAAAGGTTTGGCTCTGTGTTTGCTGGACTAATTCAATCA ACATTGTTATCTAAGAAGGAAAAGGGTGGAGAAAATGCTTCTATTAAGAAGCCTCGTGTACGTGG TTCATTTTCATTTCAAGGTGGAATGCAGACACTTGTTGACACAATGTGCAAACAGCTTGGTGAAGA TGAACTCAAACTCCAGTGTGAGGTGCTGTCCTTGTCATATAACCAGAAGGGGATCCCCTCATTAG GGAATTGGTCAGTCTCTTCTATGTCAAATAATACCAGTGAAGATCAATCTTATGATGCTGTGGTTG TCACTGCTCCAATTCGCAATGTCAAAGAAATGAAGATTATGAAATTTGGAAATCCATTTTCACTTGA CTTTATTCCAGAGGTGACGTACGTACCCCTTTCCGTTATGATTACTGCATTCAAAAAGGATAAAGT GAAGAGACCTCTTGAGGGCTTCGGAGTTCTTATCCCCTCTAAAGAGCAACATAATGGACTGAAGA CTCTTGGTACTTTATTTTCCTCCATGATGTTTCCTGATCGTGCTCCATCTGACATGTGTCTCTTTAC TACATTTGTCGGAGGAAGCAGAAATAGAAAACTTGCAAACGCTTCAACGGATGAATTGAAGCAAA TAGTTTCTTCTGACCTTCAGCAGCTGTTGGGCACTGAGGACGAACCTTCATTTGTCAATCATCTCT TTTGGAGCAACGCATTCCCATTGTATGGACACAATTACGATTCTGTTTTGAGAGCCATAGACAAGA TGGAAAAGGATCTTCCTGGATTTTTTTATGCAGGTAACCATAAGGGTGGACTTTCAGTGGGAAAA GCGATGGCCTCCGGATGCAAGGCTGCGGAACTTGTAATATCCTATCTGGACTCTCATATATACGT GAAGATGGATGAGAAGACCGCGTAA

TABLE 17 Coding Sequence for herbicide sensitive PPX2L used in certain experiments (SEQ ID NO: 47; encodes protein of SEQ ID NO: 48) ATGGTAATTCAATCCATTACCCACCTTTCACCAAACCTTGCATTGCCATCGCCATTGTCAGTTTCA ACCAAGAACTACCCAGTAGCTGTAATGGGCAACATTTCTGAGCGGGAAGAACCCACTTCTGCTAA AAGGGTTGCTGTTGTTGGTGCTGGAGTTAGTGGACTTGCTGCTGCATATAAGCTAAAATCCCATG GTTTGAGTGTGACATTGTTTGAAGCTGATTCTAGAGCTGGAGGCAAACTTAAAACTGTTAAAAAAG ATGGTTTTATTTGGGATGAGGGGGCAAATACTATGACAGAAAGTGAGGCAGAGGTCTCGAGTTTG ATCGATGATCTTGGGCTTCGTGAGAAGCAACAGTTGCCAATTTCACAAAATAAAAGATACATAGCT AGAGACGGTCTTCCTGTGCTACTACCTTCAAATCCCGCTGCACTACTCACGAGCAATATCCTTTCA GCAAAATCAAAGCTGCAAATTATGTTGGAACCATTTCTCTGGAGAAAACACAATGCTACTGAACTT TCTGATGAGCATGTTCAGGAAAGCGTTGGTGAATTTTTTGAGCGACATTTTGGGAAAGAGTTTGTT GATTATGTTATCGACCCTTTTGTTGCGGGTACATGTGGTGGAGATCCTCGATCGCTTTCCATGCA CCATACATTTCCAGAAGTATGGAATATTGAAAAAAGGTTTGGCTCTGTGTTTGCTGGACTAATTCA ATCAACATTGTTATCTAAGAAGGAAAAGGGTGGAGAAAATGCTTCTATTAAGAAGCCTCGTGTAC GTGGTTCATTTTCATTTCAAGGTGGAATGCAGACACTTGTTGACACAATGTGCAAACAGCTTGGTG AAGATGAACTCAAACTCCAGTGTGAGGTGCTGTCCTTGTCATATAACCAGAAGGGGATCCCCTCA TTAGGGAATTGGTCAGTCTCTTCTATGTCAAATAATACCAGTGAAGATCAATCTTATGATGCTGTG GTTGTCACTGCTCCAATTCGCAATGTCAAAGAAATGAAGATTATGAAATTTGGAAATCCATTTTCA CTTGACTTTATTCCAGAGGTGACGTACGTACCCCTTTCCGTTATGATTACTGCATTCAAAAAGGAT AAAGTGAAGAGACCTCTTGAGGGCTTCGGAGTTCTTATCCCCTCTAAAGAGCAACATAATGGACT GAAGACTCTTGGTACTTTATTTTCCTCCATGATGTTTCCTGATCGTGCTCCATCTGACATGTGTCT CTTTACTACATTTGTCGGAGGAAGCAGAAATAGAAAACTTGCAAACGCTTCAACGGATGAATTGAA GCAAATAGTTTCTTCTGACCTTCAGCAGCTGTTGGGCACTGAGGACGAACCTTCATTTGTCAATCA TCTCTTTTGGAGCAACGCATTCCCATTGTATGGACACAATTACGATTCTGTTTTGAGAGCCATAGA CAAGATGGAAAAGGATCTTCCTGGATTTTTTTATGCAGGTAACCATAAGGGTGGACTTTCAGTGG GAAAAGCGATGGCCTCCGGATGCAAGGCTGCGGAACTTGTAATATCCTATCTGGACTCTCATATA TACGTGAAGATGGATGAGAAGACCGCGTAA

DISCUSSION

While PPO inhibitor-resistant plants have been generated through genetic engineering approaches (Choi, 1998; Lee, 2000; Lermontova. 2000; Ha, 2004; Jung, 2004; Lee, 2004; Li, 2005), A. tuberculatus populations have developed resistance from the repeated use of these herbicides in agronomic production systems. The consequence of A. tuberculatus evolving resistance to PPO inhibitors, combined with its already widespread resistance to ALS-inhibiting herbicides, is that the only remaining chemical option for its control following emergence in Glycine max (soybean) production systems is glyphosate, which requires the planting of glyphosate-resistant varieties (Patzoldt, 2005). Although the molecular mechanisms of evolved resistance to many herbicides have been identified, such has not yet been elucidated for resistance to PPO inhibitors.

Seven different mechanisms of PPO inhibitor resistance have been proposed for plants (Dayan, 1997). Two of these mechanisms include either enhanced metabolic degradation of the herbicide or an alteration of the herbicide target site, which together constitute the majority of mechanisms for herbicide resistance in weed species. Of these, an altered herbicide target enzyme (PPO) was investigated based on previous characterization of R A. tuberculatus plants (Patzoldt, 2004). It was later determined in an independently identified PPO inhibitor-resistant A. tuberculatus population that enhanced metabolism was not responsible for resistance (Shoup, 2005).

The mechanism of PPO inhibitor resistance that was selected within natural populations of A. tuberculatus populations was a codon deletion in a gene encoding PPO. While alterations of herbicide target proteins are common mechanisms for conferring resistance, several characteristics about this specific mechanism merit highlighting. First, PPO inhibitors have two herbicide target sites in plants; i.e., in plastids and mitochondria (Jacobs, 1984); therefore, in order for target-site resistance to occur, two altered genes would need to be selected. However, A. tuberculatus plants have overcome this obstacle via mutation in a single gene (PPX2L) that encodes both plastidic and mitochondrial PPO isoforms. Second, the specific alteration of PPO2L that confers resistance to PPO-inhibiting herbicides is an amino acid deletion resulting from a three-bp deletion in the genomic (coding) DNA. This is the first report of an amino acid deletion, rather than a substitution, in a herbicide target site being selected in a natural (field) population as a resistance mechanism. While intentional selection for resistance to PPO inhibitors identified amino acid substitutions that conferred resistance (Li, 2005; U.S. Pat. No. 5,939,602), the codon-deletion approach revealed by A. tuberculatus is instructive of an alternative approach to achieve resistance. Third, the R biotype was found to be resistant to multiple chemical families of PPO inhibitors, albeit at different levels (Patzoldt, 2005), indicating that the ΔG210 mutation confers resistance to all PPO inhibitors. Finally, that R A. tuberculatus plants lacked one of the PPO genes (PPX2) found in plants from the S biotype is curious and requires further research. However, the absence of PPX2 in the R biotype likely is not related to the resistance phenotype since resistance was (incompletely) dominant and exhibited single-locus inheritance, PPX2L co-segregated with resistance, and the ΔG210 mutation was sufficient to confer lactofen insensitivity.

While the origin of the G210 codon deletion of PPX2L identified in the R A. tuberculatus biotype is uncertain, nucleotide length polymorphisms are not uncommon in this plant species. Codon insertion/deletions (indels) among populations of A. tuberculatus were previously identified in other genes encoding herbicide target proteins, e.g., ALS, and EPSPS (5-enolpyruvylshikimate-3-phosphate synthase. Furthermore, other indels, in addition to the G210 indel, were found among PPX genes in this study. In PPX1 (see SEQ ID NOs:13 and 14 and SEQ ID NO19 and 20 and GenBank Accession Nos. DQ386112 and DQ386115), there were two additional, adjacent proline codons in the nucleotide sequence from R plants relative to S plants. An indel was also identified when PPX2 was compared with PPX2L from S plants (See SEQ ID NOs: 19-20 and 21-22; NCBI Accession Nos. DQ386113 and DQ386114). As observed for the G210 polymorphism between R and S PPX2Ls, this also resulted in a glycine amino acid indel, but was located at a different position (128 nucleotides downstream of the G210 codon). The codon indels observed in A. tuberculatus typically are associated with short, simple sequence repeats (SSRs). The G210 indel in PPX2L is part of a bi-GTG repeat (or a bi-TGG repeat), the PPX2/PPX2L indel is part of a tri-GGA repeat, and the PPX1 indel is part of a hexa-CCT repeat. SSRs are recognized as a means to provide adaptive genetic variation for evolutionary processes because of their high mutability (Kashi, 2006). Although the numbers of repeats associated with some of the PPX indels are fewer than typically recognized for SSRs that the indels are found within repeated nucleotides suggests a means for their evolutionary origin.

In regards to PPO inhibitor-resistant A. tuberculatus in agro-ecosystems, resistance can be transmitted maternally and paternally, and therefore is able to spread through seed dispersal or, more rapidly, via wind dispersal of pollen. Since A. tuberculatus is a dioecious plant, it is forced to outcross. This obligate outcrossing, combined with a significant level of resistance that is expressed in the heterozygous state (FIG. 2), will make pollen a very effective means for dissemination of the resistance. In addition to dissemination from a single “source” population, resistance to PPO inhibitors could become more widespread in A. tuberculatus populations by independent selection events. In fact, it seems likely that this already has occurred given the distinct locations where PPO inhibitor-resistant populations have been identified (Shoup, 2003; Li, 2004; Patzoldt, 2005), and the different PPX2L alleles containing the ΔG210 mutation identified in this study (FIG. 7).

A. tuberculatus is one of the most problematic weeds in agronomic fields throughout the Midwestern United States. In particular, the propensity of A. tuberculatus to rapidly evolve herbicide resistance makes its management difficult (Patzoldt, 2004). The herbicide resistance mechanism reported herein illustrates the sophisticated means by which it can adapt and evolve in response to weed control efforts. With the loss of PPO inhibitors as an effective A. tuberculatus management tool in soybean, farmers may become even more reliant on glyphosate.

In summary, an altered herbicide target site confers PPO inhibitor resistance in the R biotype. Several unique characteristics about this herbicide resistance mechanism deserve mention. First, PPO inhibitors have two herbicide target sites in plants (i.e. plastids and mitochondria (Jacobs and Jacobs, 1984); therefore, in order for target-site resistance to occur, two altered genes would need to be selected. Without wishing to be bound by theory, the inventors believe that plants from the R waterhemp biotype have overcome this obstacle with natural selection of a mutation in a single gene (PPX2L) that encodes two proteins that theoretically function in both plastids and mitochondria. Second, the specific alteration of PPO2 that confers resistance to PPO-inhibiting herbicides is an amino acid deletion rather than a substitution, unlike prior art mutations (see, e.g., U.S. Pat. Nos. 6,282,837; 5,939,602; and 6,808,904). Substitution mutations, in addition to the Gly deletion, have been observed in naturally resistant waterhemp.

The examples provided herein are for illustrative purposes and are not intended to limit the scope of the invention as claimed. Any variations in the exemplified compositions, plants and methods which occur to the skilled artisan are intended to fall within the scope of the present invention.

EXAMPLES

Detailed procedures for generation and analysis of A. tuberculatus lines, herbicide dose-response, and calculation of degree of dominance experiments and certain other procedures follow.

Example 1 A. tuberculatus Biotypes

The R biotype used in this study was derived from an A. tuberculatus (waterhemp) population originally collected in Adams County, Illinois, and confirmed resistant to PPO-, ALS-, and photosystem II-inhibiting herbicides (Patzoldt, 2005). The S biotype was collected in Wayne County, Illinois, and was identified in previous experiments to be susceptible to all herbicides tested (Patzoldt, 2002). A. tuberculatus plants derived from the original Adams County population that were PPO inhibitor-susceptible (S-BioAC), and those from a PPO inhibitor-resistant biotype collected in Clinton County, Illinois (R-BioCC), were utilized for sequencing of PPX2L alleles only.

Example 2 Plant Culture

A. tuberculatus seeds for each experiment were sown in flats (surface area of 930 cm²) containing a 1:1:1 mixture of soil:peat:sand. Seedlings for each experiment were transplanted when needed into 12-cm square pots containing 800 ml of soil plus 0.2% (by vol) 14-14-14 Nutricote (Agrivert Inc., Glenpool, Okla.) when they were approximately 1-cm in height. Plants were grown in a greenhouse maintained at 28/22° C. day/night with supplemental light (minimum of 800 μmol m⁻² s⁻¹ photon flux at the plant canopy) provided by mercury halide and sodium vapor lamps programmed for a 16-hour photoperiod.

Example 3 Herbicide Applications

Herbicide treatments were applied using a compressed air, moving nozzle laboratory sprayer equipped with an 80° flat fan nozzle (Teejet, Spraying Systems Co, Wheaton, Ill.) delivering 187 L ha⁻¹ of water at 207 kPa. The nozzle was maintained approximately 45 cm above the plant canopy. Plants were returned to the greenhouse immediately after herbicide treatment. All foliar-applied herbicide treatments were made when A. tuberculatus plants were 10-12 cm in height.

Example 4 Generation of F₁, F₂, and BC Lines

To create F₁ lines, A. tuberculatus plants from the R biotype were crossed with plants from the S biotype. Plants from the R biotype were confirmed herbicide-resistant by treatment with a herbicide mixture containing lactofen at 175 g active ingredient (ai) ha⁻¹, imazamox at 44 g acid equivalent (ae) ha⁻¹, and atrazine at 1000 g ai ha⁻¹, a PPO, acetolactate synthase (ALS), and photosystems II (PSII) inhibitor, respectively, plus 1% (by vol) crop oil concentrate (COC; Herbimax, Loveland Industries) and 2.5% (by vol) ammonium sulfate (AMS; Agriliance, St. Paul, Minn.). F₁ lines were created where the maternal parent was either S {F₁(S)} or R {F₁(R)}. Following maturity, seeds were harvested from each female individually as full-sib lines. F₁ male plants were crossed with female plants from the S biotype, R biotype, or F₁ full-sibs to create BC_(E), BC_(R), or F₂ lines, respectively. Separate crosses were conducted using males from F₁(S) or F₁(R) lines. All F1 plants used for crossing were confirmed herbicide-resistant by treating with a mixture of lactofen, imazamox and atrazine as described herein. Each genetic combination was conducted twice with new A. tuberculatus plants, thus constituting a complete replication of the experiment. Crosses were conducted in growth chambers maintained at 28/22° C. day/night with fluorescent and incandescent bulbs providing 400 μmol m⁻² s⁻¹ photon flux at the plant canopy programmed for a 16-hour photoperiod.

Example 5 Evaluation of F₂ and BC Lines

To confirm that F₁ lines were uniform in response, A. tuberculatus plants from F₁(S), F₁(R), R-parent, or S-parent lines were treated with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) COC when they were 10-12 cm in height. Plants were qualitatively assessed 15 days after treatment as either R or S, followed by removal of above-ground tissue, drying at 65° C. for at least three days, and weighing to obtain dry mass measurements. A. tuberculatus lines were evaluated in a completely randomized design with 100 replications (plants) per line. Dry weight measurements of lactofen-treated plants were compared with control plants from the same line that received an application of 1% (by vol) COC only. Data from F₁ lines were compared to the parental biotypes and analyzed using PROC GLM in SAS (SAS Systems Inc.) using single degree of freedom contrast statements.

When analyzed, the R parent and both F₁ lines were significantly different from the S-parent in their response to lactofen at 110 g ai ha⁻¹ (P<0.0001). Furthermore, both F₁(S) and F₁(R) lines were significantly different from the R-parent (P=0.0009 or P=0.0008, respectively), but were not different from one another (P=0.9790). Even though F₁ lines were significantly different from the R-parent when comparing mean responses, individual heterozygous plants could not be distinguished from homozygous R plants due to their wide overlap of responses (FIG. A6). These results demonstrated that treatments with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) COC were able to distinguish lactofen-susceptible plants based on dry weights, and were useful for determining the inheritance of PPO inhibitor resistance in F₂ and backcrossed (BC) lines.

Inheritance of PPO inhibitor resistance was determined by evaluating R or S responses of plants from F₂ and BC lines 15 days after treatment with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) COC. From each F₂ or BC line, 50 plants from each cross (including replicated crosses) were assessed in a completely randomized design. The entire experiment was conducted twice, with a total of 100 plants assessed from each cross. Responses of each cross were subjected to Chi-square analysis to determine if responses were due to the inheritance of a single genetic unit of inheritance. No differences were observed among replications of the same cross; therefore, data obtained from similar crosses were combined.

Alternatively, waterhemp plants from F₁(S), F₁(R), R-parent, or S-parent lines were treated with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) COC when they reached 10-12 cm in height. Plants were qualitatively assessed 15 days after treatment as either R or S, followed by removal of above-ground tissue, drying at 65° C. for at least three days, and weighing to obtain dry mass measurements. Waterhemp lines were evaluated in a completely randomized design with 100 replications (plants) per line. Dry weight measurements of lactofen-treated plants were compared with control plants from the same line that received an application of 1% (by vol) COC only. Data from F₁ lines were compared to the parental biotypes and analyzed using PROC GLM in SAS software (SAS Institute, Cary, N.C.) using single degree of freedom contrast statements.

Example 6 Calculation of Degree of Dominance

A. tuberculatus plants from the F₁(S) or F₁(R) lines, including plants from the S or R parental biotypes, were treated with various rates of lactofen or acifluorfen to calculate dominance of PPO inhibitor resistance. Herbicides were applied at rates incrementally spaced along a base 10 logarithmic scale. Herbicide rates for acifluorfen and lactofen for each A. tuberculatus line were: 0.00022 to 220 g ai ha⁻¹ for the S-parent; 0.00022 to 22000 g ai ha⁻¹ for F₁s; and 0.0022 to 22000 g ai ha⁻¹ for the R-parent.

Herbicide treatment dispersions with acifluorfen or lactofen included 1% (by vol) COC. Herbicide dose-response experiments were conducted using a completely randomized design with six replications per treatment. Both sets of F₁s (including reciprocals) were used in dose-response experiments, thus constituting a complete replication. Above-ground tissue from all herbicide dose-response experiments with acifluorfen was harvested 10 days after treatment (DAT), while tissue treated with lactofen was harvested either 10 or 15 DAT. Plant material was dried at 65° C. for at least three days, and dry weights recorded. SAS was used to analyze differences between experimental runs using PROC GLM, and GR₅₀ (growth reduction by 50%) estimates were calculated using PROC NLIN using percent dry weight values compared with control plants (Seefeldt et al. 1995). Control plants from each A. tuberculatus line received a treatment solution containing 1% (by vol) COC only. The degree of dominance (D) for PPO inhibitor resistance was calculated using the formula D=(2W₃−W₂−W₁)/(W₂−W₁), where W₁=log(GR₅₀) of the S-parent, W₂=log(GR₅₀) of the R-parent, and W₃=log(GR₅₀) of the F₁(S) or F₁(R) lines (0 to 1=dominant; 0=partially dominant; 0 to −1=recessive) (Stone, 1968).

Waterhemp plants from the F₁(S) or F₁(R) lines, plus plants from the S or R parents, were treated with lactofen or acifluorfen when they reached 10 to 12 cm in height. Herbicides were applied at rates incrementally spaced along a base 10 logarithmic scale. Herbicide rates for acifluorfen and lactofen for each waterhemp line were: 0.00022 to 220 g ai ha⁻¹ for the S-parent; 0.00022 to 22000 g ai ha⁻¹ for F₁s; and 0.0022 to 22000 g ai ha⁻¹ for the R-parent. Herbicide treatment dispersions with acifluorfen or lactofen included 1.0% (by vol) COC.

Herbicide dose-response experiments were conducted using a completely randomized design with six replications per treatment. Both sets of F₁s (including reciprocals) were used in dose-response experiments, thus constituting a complete replication. Above-ground tissue from all herbicide dose-response experiments with acifluorfen was harvested 10 days after treatment (DAT), while those treated with lactofen were harvested either 10 or 15 DAT. Plant material was dried at 65° C. for at least three days, and dry weights recorded. SAS (statistical software package, SAS Institute Inc., Cary, N.C.) was used to analyze differences between experimental runs using PROC GLM, and GR₅₀ (growth reduction by 50%) estimates were calculated using PROC NLIN as described by Seefeldt et al. (1995) using percent dry weight values compared with control plants. Control plants from each waterhemp line received a treatment solution containing 1% (by vol) COC only. The degree of dominance (D) for PPO inhibitor resistance was calculated using the formula D=(2W₃−W₂−W₁)/(W₂−W₁), where W₁=log(GR₅₀) of the S-parent, W₂=log(GR₅₀) of the R-parent, and W₃=log(GR₅₀) of the F₁(S) or F₁(R) lines (0 to 1=dominant; 0=partially dominant; 0 to −1=recessive) (Stone 1968).

Example 7 cDNA Sequencing

Total RNA was isolated using young leaf tissue from a single plant from each of the R and S biotype (McCarty, 1986), followed by purification of mRNA (Promega, Madison, Wis.). Upon sequencing PPX2 from the S biotype, two transcripts were identified of different length; these were designated as PPX2S or PPX2L for short or long forms, respectively.

Purified mRNA was used to obtain full-length sequences of PPX1 or PPX2 using 5′ and 3′ RACE (Rapid Amplification of cDNA Ends, Invitrogen, Carlsbad, Calif.). Primers were designed based on conserved regions of nucleotide sequences of PPX1 or PPX2 from numerous plant species (Che et al. 2000; Horikoshi et al. 1999; Johnston et al. 1998; Lermontova et al. 1997; Narita et al. 1996; Watanabe et al. 2001). Sequencing of the resultant fragments facilitated the design of gene-specific primers for A. tuberculatus PPX1 and PPX2 that were used to obtain their full-length sequences.

Total RNA was individually isolated from three A. tuberculatus plants each of the R or S biotypes, and used to create cDNA in reactions with reverse transcriptase (Invitrogen). PCR was used to amplify PPX1, PPX2, or PPX2L with the following primers: PPX1, forward 5′-gagagagtgcgagagagatgag-3′ (SEQ ID NO:1) and reverse 5′-caagatgctggagccctattgac-3′ (SEQ ID NO:2); PPX2, forward 5′-gccatcgccattgtcagtttac-3′ (SEQ ID NO:3) and reverse 5′-gaattacgcggtcttctcatccat-3′ (SEQ ID NO:4); PPX2L, forward 5′-gacaaaattggattcagaatttagc-3′ (SEQ ID NO:5) and reverse 5′-gaattacgcggtcttctcatccat-3′ (SEQ ID NO:6). PCRs contained 1 μl cDNA, 400 nM each of forward and reverse primers, 0.2 mM each of dATP, dCTP, dGTP, and dTTP, 1.5 mM MgCl₂, and 1.0 unit of High Fidelity Taq polymerase (Roche Molecular Biochemicals, Indianapolis, Ind.) with a 1× concentration of supplied buffer in a final volume of 25 μl. The reactions were subjected to a 3 min incubation at 95° C.; 35 cycles of 0.5 min at 95° C., 1 min at 58° C., and 1.5 min at 72° C.; then 5 min at 72° C. Resultant PCR products were isolated by gel electrophoresis, sequenced (Patzoldt, 2001), and compared using both Sequencher 4.1™ (Gene Codes Corporation, Ann Arbor, Mich.) and online software (described in Thompson et al. 1994. Nucl. Acids Res. 22:4673-4690). Sequences among plants from the same biotypes were similar: therefore, only a single sequence is presented for each gene/biotype combination.

Example 8 Southern Blot

Genomic DNA (gDNA) was isolated from young leaves of A. tuberculatus plants from the S or R biotypes (Ausubel, 1999). PPO inhibitor responses of each plant were confirmed by treatment with lactofen at 175 g ai ha⁻¹ plus 1% (by vol) COC. Samples were prepared by digesting 7.5 μg gDNA with 100 units of either EcoRI or HindIII to completion, followed by separation in a 1% (by wt) agarose gel, and then transferred to a nylon membrane (Roche Molecular Biochemicals, Indianapolis, Ind.). The membrane was probed with a DIG-labeled (Roche Molecular Biochemicals) PCR fragment of PPX2L amplified from gDNA isolated from a single S plant. Hybridization and probe detection were performed following the manufacturer's instructions.

Example 9 PCR-Based Molecular Markers

Inheritance of PPX1 and PPX2L alleles in BC_(s) progeny was studied by treating plants with lactofen at 110 g ai ha⁻¹ plus 1% (by vol) COC when they were 10-12 cm in height. Prior to lactofen applications, tissue samples were obtained from each plant to isolate DNA (Doyle and Doyle, 1990). PCR-based molecular markers were used to identify the parental origin (R or S) of the PPX alleles contributed by the F₁ male to the BC_(s) progeny.

To differentiate R or S PPX1 alleles, a fragment of genomic PPX1 was amplified via PCR using the forward primer, 5′-tgataagtcgctcaatggaga-3′ (SEQ ID NO:7), and reverse primer 5′-agatttgtagcacctccaatg-3′ (SEQ ID NO:8), followed by BspDI digestion to identify S alleles (i.e., S PPX1 alleles contain a recognition sequence for BspDI, while R alleles do not).

To identify parent-specific PPX2L alleles, a fragment of genomic PPX2L was amplified via PCR using the forward primer, 5′-aagagacctcttgagggcttc-3′ (SEQ ID NO:9), and reverse primer 5′-gaattacgcggtcttctcatccat-3′ (SEQ ID NO:10), followed by Tfil digestion to identify S alleles (i.e., S PPX2L alleles contain a recognition sequence for Tfil, while R alleles do not). PCRs contained 40 ng total DNA, 400 nM each of forward and reverse primers, 0.2 mM each of dATP, dCTP, dGTP, and dTTP, 2.0 mM MgCl₂, and 1 unit of Taq polymerase (Invitrogen) with a 1× concentration of supplied buffer in a final volume of 20 μl. The reactions were subjected to a 3 min incubation at 95° C.; 40 cycles of 0.5 min at 95° C., 1 min at 60° C. or 64° C. for reactions with PPX1 or PPX2L primers, respectively, and 1.5 min at 72° C.; then 5 min at 72° C. Following PCR amplification, a mixture containing 0.5 unit of the appropriate restriction enzyme with a 1× concentration of supplied buffer in a final volume of 10 μl was added to each reaction. Digests with BspDI were incubated at 37° C. for four hrs, while digests with Tfil were incubated at 65° C. for two hrs. PCR products were fractionated in a 1% (by wt) agarose gel containing 0.5 μg ml⁻¹ ethidium bromide and visualized with ultraviolet light.

Example 10 PPX2L Genomic DNA Sequencing

gDNA was isolated from leaf tissue of S or R plants (37) to sequence a portion of genomic PPX2L. Primers were designed that flanked the G210 codon of PP02L, then subsequent sequencing of amplified fragments facilitated the design of new primers until the exon containing the G210 codon was identified. Primer sets (A-D), starting with the largest fragment, were (forward then reverse): A, 5′-gccatcgccattgtcagtttac-3′ (SEQ ID NO:3) and 5′-ggagcagtgacaaccacagcatca-3′ (SEQ ID NO:36); B, 5′-atcgatgatcttgggcttcgtg-3′ (SEQ ID NO:37) and 5′-aatggtaaggagtcgcaccaac-3′ (SEQ ID NO:38); C, 5′-cttcaaatcccgctgcacta-3′ (SEQ ID NO:39) and 5′-tacttctggaaatgtatgg-3′ (SEQ ID NO:40) and D, 5′-gagaaaacacaatgctactgaa-3′ (SEQ ID NO:41) and 5′-acagcctccagaaaatgttg-3′ (SEQ ID NO:42). PCR amplification, sequencing, and analysis were similar to the method used for cDNA sequencing of PPX genes.

Example 11 Functional Complementation

A shortened version of PPX2L from the S A. tuberculatus biotype was cloned into a pBAD-TOPO expression vector (Invitrogen) so that translation began at the second ATG start codon (+91). PPX2L cDNA was PCR-amplified using the forward primer 5′-caggaataagtaatgggcaacatttctgag-3′ (SEQ ID NO:11) containing both a ribosome binding site (AGGA) and ATG start codon, and reverse primer 5′-gaagaattacgcggtcttctcatc-3′ (SEQ ID NO:12) containing a stop codon. In order to create PPO inhibitor R and S plasmids that would encode proteins differing only in the presence/absence of G210, PPX2L was PCR-amplified from multiple cDNA samples and a region of the gene encompassing an approximately 500-bp XhoI/DraIII fragment was sequenced. The 3-bp polymorphism corresponding to the ΔG210 mutation was within this XhoI/DraIII fragment. Two XhoI/DraIII fragments were identified that were identical except for the presence/absence of the G210 codon and a C/T nucleotide polymorphism that was in the third position of a serine codon (and therefore did not alter the encoded protein). These two fragments were each used to replace the corresponding fragment in the pBAD-TOPO PPX2L construct. The region encompassing the replaced fragment was sequenced from the two resulting constructs to confirm the existence of the 3-bp polymorphism, and that no other polymorphisms were created during the cloning process.

Susceptible and R PPO plasmids were used to transform a hemG mutant strain of E. coli, SASX38 (Sasarman, 1979). The SASX38 E. coli strain was maintained on LB media supplemented with 20 μg ml⁻¹ hematin. Transformation-competent E. coli were prepared using CaCl₂ (Sambrook, 1989). Transformed colonies of SASX38 and non-transformed controls were tested for their ability to grow on LB media alone or supplemented with 20 μg ml⁻¹ hematin or with the PPO inhibitor lactofen ranging from 0.01 to 100 μM, and incubated at 37° C. for 14 hrs.

Example 12 Herbicide-Tolerant Plants by Overexpression of Plant PPO Genes

To express the herbicide resistant PPO from waterhemp in transgenic plants, the appropriate full length cDNA is inserted into a plant expression vector, desirably under the regulatory control of a plant expressible, constitutive promoter and desirably a binary vector suitable for Agrobacterium tumefaciens mediated transformation of plant cells, plant tissue. The resulting plasmid is transformed into a suitable A. tumefaciens strain. See, e.g. Uknes et al. 1993. Plant Cell 5:159-169.

Leaf disks of Nicotiana tabacum cv. Xanthi-nc are infected with A. tumefaciens harboring the herbicide resistant PPO expression vector generally as described by Horsch et al. 1985. Science 227: 1229. Kanamycin-resistant shoots from 15 independent leaf disks are transferred to rooting medium, transplanted to soil and the resulting plants are grown to maturity in the greenhouse. Seeds from these plants are collected and germinated on MS agar medium containing kanamycin. Multiple individual kanamycin resistant seedlings from each independent primary transformant are grown to maturity in the greenhouse, and their seed collected. These seeds are germinated on MS agar medium containing kanamycin.

Plant lines that give rise to exclusively kanamycin resistant seedlings are homozygous for the inserted gene and are subjected to further analysis. Leaf disks of each of the 15 independent transgenic lines are excised with a paper punch and placed onto MS agar containing various increasing concentrations of a PPO inhibitory herbicide. After three weeks, two sets of 10 disks from each line are weighed, and the results recorded. Transgenic lines more resistant to the inhibitor than wild type (non-transformed) plants are selected for further analysis.

RNA is extracted from leaves of each of these lines. Total RNA from each independent homozygous line, and from non-transgenic control plants, is separated by agarose gel electrophoresis in the presence of formaldehyde (Ausubel et al. 1989. Current Protocols in Molecular Biology, Wiley & Sons, New York). The gel is blotted to nylon membrane (Ausubel et al., supra.) and hybridized with the radiolabeled Arabidopsis protox cDNA. Hybridization and washing conditions are as described by Church and Gilbert. 1984. Proc. Natl. Acad. Sci. USA 81:1991-1995. The filter is analyzed by autoradiography, and intense RNA bands corresponding to the protox transgene are detected in all herbicide-tolerant transgenic plant lines.

To further evaluate resistance of the protox-overexpressing line, plants are grown in the greenhouse and treated with various concentrations of a protox-inhibiting herbicide.

Example 13 Growth of Tobacco Cells in Suspension Culture Media

MX1 medium consists of Murashige and Skoog (“MS”, T. Murashige et al. 1962. Physiol. Plant. 15:473-497) major salts, minor salts and Fe-EDTA (Gibco #500-1117; 4.3 g/l), 100 mg/l myo-inositol, 1 mg/l nicotinic acid, 1 mg/l pyridoxine-HCl, 10 mg/l thiamine—HCl, 2-3 g/l sucrose, 0.4 mg/l 2,4-dichlorophenoxyacetic acid, and 0.04 mg/l kinetin, pH 5.8. The medium is sterilized by autoclaving.

N6 medium comprises macroelements, microelements and Fe-EDTA as described by C-C. Chu et al. 1075. Scientia Sinica 18:659, and the following organic compounds: pyridoxine-HCl (0.5 mg/l), thiamine-HCl (0.1 mg/l), nicotinic acid (0.5 mg/l), glycine (2.0 mg/l), and sucrose (30.0 g/l). The solution is autoclaved. The final pH is 5.6.

Macroelements are made up as a 10× concentrated stock solution, and microelements as a 1000× concentrated stock solution. Vitamin stock solution is normally prepared 100× concentrated. Suspension cultured cells of Nicotiana tabacum, line S3, are grown in liquid culture medium MX1. 100 ml Erlenmeyer flasks containing 25 ml medium MX1 are inoculated with 10 ml of a cell culture previously grown for 7 days. Cells are incubated at 25° C. in the dark on an orbital shaker at 100 rpm (2 cm throw). Cells are subcultured at 7 day intervals by inoculating an aliquot sample into fresh medium, by decanting or pipetting off around 90% of the cell suspension followed by replenishing fresh medium to give the desired volume of suspension. 5-8 grams of fresh weight cell mass are produced within 10 days of growth from an inoculum of 250-350 mg cells.

Example 14 Production of Tobacco Cell Cultures Tolerant to Herbicidal PPO

Inhibitors by Plating Cells on Solidified Selection Medium

Cells are pregrown and harvested by allowing cells to sediment, or by brief centrifugation at 500×g, and the spent culture medium is removed. Cells are then diluted with fresh culture medium to give a cell density suitable for cell plating, about 10,000 colony forming units per ml. For plating, cells in a small volume of medium (approx. 1 ml) are evenly spread on top of solidified culture medium (MX1, 0.8% agar) containing the desired concentration of the inhibitor. About 20-30 ml of medium are used per 10 cm Petri plate. The suitable inhibitor concentration is determined from a dose-response curve, and is at least twofold higher than the IC₅₀ of sensitive wild-type cells. Transgenic plant cells carrying either the wild type waterhemp or the resistant waterhemp PPO are compared with respect to their properties.

Culture plates containing cells spread onto selection medium are incubated under normal growth conditions at 25-28° C. in the dark until colonies are formed. Emerging colonies are transferred to fresh medium containing the inhibitor in the desired concentration. In a modification of the described method, the pregrown suspension of cultured cells is first spread in a small volume of liquid medium on top of the solidified medium. An equal amount of warm liquid agar medium (1.2-1.6% agar) kept molten at around 40° C. is added and the plate gently but immediately swirled to spread the cells evenly over the medium surface and to mix cells and agar medium, before the medium solidifies.

Alternatively, the cells are mixed with the molten agar medium prior to spreading on top of the selection medium. This method has the advantage that the cells are embedded and immobilized in a thin layer of solidified medium on top of the selection medium. It allows for better aeration of the cells as compared to embedding cells in the whole volume of 20-30 ml.

Example 15 Production of Tobacco Cell Cultures Tolerant to an Herbicidal PPO Inhibitor by Growing Cells in Liquid Selection Medium

Cells cultured as described above are inoculated at a suitable cell density into liquid medium MX1 containing the desired concentration of an herbicidal PPO inhibitor. Cells are incubated and grown as described above. Cells are subcultured, as appropriate depending on the rate of growth, using fresh medium containing the desired inhibitor concentration after a period of 7-10 days. Depending on the inhibitor concentration used, cell growth may be slower than in the absence of inhibitor.

Example 16 Production of Tobacco Cells with Enhanced Levels of PPO Enzyme

To obtain cell cultures or callus with enhanced levels of an herbicide resistant PPO of the present invention, transgenic suspension cultures or callus are transferred, in a step-wise manner, to increasingly higher concentrations of an herbicidal PPO inhibitor. In particular, the following steps are performed:

Colonies emerging from plated cells are transferred to liquid MX1 medium containing the same concentration of PPO inhibitor as used in the selection described above in order to form suspension cultures. Alternatively, selected cell suspension cultures are subcultured in liquid MX1 medium containing the same concentration of PPO inhibitor as used for selection as set forth above.

Cultures are subcultured 1-20 times at weekly intervals, and they are then subcultured into MX1 medium containing the next higher herbicide concentration. The cells are cultured for 1-10 subcultures in medium containing this higher concentration of herbicide. The cells are then transferred to MX1 medium containing the next higher concentration of herbicide.

Alternatively, pieces of selected transgenic callus are transferred to solidified MX1 medium supplemented with the desired herbicide concentration. Transfer to higher herbicide concentrations follows the procedure outlined in the preceding paragraph except that solidified medium is used.

Example 17 Herbicide Dose-Dependent Growth of Cells in Suspension Cultures

To establish a dose-response curve, the growth of cells in medium in the presence of different concentrations of herbicide is determined. Suspension culture cells of herbicidal PPO inhibitor sensitive wild-type tobacco cells S3 and herbicide tolerant transgenic cells are pregrown in liquid medium at high cell density for 2-4 days. The cells are washed free of spent medium; fresh medium without herbicide is added to give the desired cell density (about 150 mg fresh weight, FW) cells per ml of suspension). A 2.5 ml aliquot of cell suspension, containing approx. 250-300 mg fresh weight (FW) cells, is inoculated into about 30 ml of liquid medium with the desired herbicide concentration contained in a 100 ml Erlenmeyer flask. Care is taken to inoculate the same amount of cells into each flask. Each flask contains an equal volume of medium. 3-6 replicate flasks are inoculated per herbicide concentration. The herbicide concentrations are zero (=control), 0.1 ppb, 0.3 ppb, 1 ppb, 3 ppb, 10 ppb, 30 ppb, 100 ppb, 300 ppb, 1000 ppb, 3000 ppb, and 10,000 ppb. Samples of inoculum are also analyzed to determine the mass of cells inoculated per flask.

Cells are then incubated for growth under controlled conditions at 28° C. in the dark for 10 days. The cells are harvested by pouring the contents of each flask onto a filter paper disk attached to a vacuum suction device to remove all liquid and to obtain a mass of reasonably dry fresh cells. The fresh mass of cells is weighed. The dry weight of samples may be obtained after drying.

Cell growth is determined and expressed as relative cell gain within 10 days and expressed as a percentage relative to cells grown in the absence of herbicide according to the formula: (final mass of herbicide-grown cells minus inoculum mass.times.100 divided by final mass of cells grown without herbicide minus inoculum mass). IC₅₀ values are determined from graphs of plotted data (relative cell mass vs. herbicide concentration). IC₅₀ denotes the herbicide concentration at which cell growth is 50% of control growth (cells grown in the absence of herbicide).

In a modification of the method several pieces of transgenic callus derived from a herbicide resistant cell culture, obtained as described above, are transferred to solidified callus culture medium containing the different herbicide concentrations. Relative growth is determined after a culture period of 2-6 weeks by weighing callus pieces and comparing to a control culture grown in medium without herbicide. However, the suspension culture method has its greater accuracy.

Example 18 Determination of Cross Tolerance

To determine the extent at which cells show tolerance to analogous or other herbicides, cells are grown in increasing concentrations of chosen herbicides. The relative growth of the cells and their IC₅₀ value is determined for each herbicide for comparison.

Example 19 Determining the Stability of the Herbicide Tolerance Phenotype

To determine whether the herbicide resistant phenotype of a cell culture is maintained over time, cells are transferred from herbicide-containing medium to medium without herbicide. Cells are grown as described above in the absence of herbicide for a period of 3 months, employing regular subcultures at suitable intervals (7-10 days for suspension cultures; 3-6 weeks for callus cultures). A known quantity of cells is then transferred back to herbicide-containing medium and cultured for 10 days (suspension cultures) or 4 weeks (callus cultures). Relative growth is determined as described above.

Example 20 Production of Herbicide Resistant Corn

Ears are harvested from self pollinated corn plants of a line of corn susceptible to transformation and regeneration 12-14 days post pollination. Husks are removed, and the ears are sterilized for about 15 minutes by shaking in a 20% solution of commercial bleach (5% sodium hypochlorite) solution with detergent added for better wetting. Ears are then rinsed several times with sterile water. All further steps are performed aseptically in a sterile air flow hood. Embryos (1.5-2.5 mm in length) are removed from the kernels with a spatula and placed, embryo axis downward, onto solid MS culture medium containing 2 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D), 3% sucrose, solidified with 0.24% gellan gum.

Embryogenic callus forms on the scutellum tissue of the embryos within 2-4 weeks of culture at about 28° C. in the dark. The callus is removed from the explant and transferred to fresh solidified MS medium containing 2 mg/l 2,4-D. The subculture of embryogenic callus is repeated at weekly intervals. Only callus portions having an embryogenic morphology are subcultured. The cultured callus tissue is transformed with the resistant PPO of the present invention.

Plants are regenerated from the selected embryogenic callus cultures by transferring to fresh regeneration medium. Regeneration media used are: ON6 medium consisting of N6 medium lacking 2, 4-3, or N61 consisting of N6 medium containing 0.25 mg/l 2,4-D and 10 mg/l kinetin (6-furfurylaminopurine), or N62 consisting of N6 medium containing 0.1 mg/l 2,4-D and 1 mg/l kinetin, all solidified with 0.24% gellan gum. Cultures are grown at 28° C. in the light (16 h per day of 10-100 μEinsteins/m² sec from white fluorescent lamps). The cultures are subcultured every two weeks onto fresh medium. Plantlets develop within 3 to 8 weeks. Plantlets at least 2 cm tall are removed from adhering callus and transferred to root promoting medium. Different root-promoting media are used. The media consist of N6 or MS medium lacking vitamins with either the usual amount of salts or with salts reduced to one half, sucrose reduced to 1 g/l, and further either lacking growth regulating compounds or containing 0.1 mg/l α-naphthaleneacetic acid. Once roots are sufficiently developed, plantlets are transplanted to a potting mixture consisting of vermiculite, peat moss and garden soil. At transplanting all remaining callus is trimmed away, all agar is rinsed off and the leaves are clipped about half. Plantlets are grown in the greenhouse initially covered for some days with an inverted clear plastic cup to retain humidity and grown with shading. After acclimatization plants are repotted and grown to maturity. Fertilizer Peters 20-20-20 is used to ensure healthy plant development. Upon flowering plants are pollinated, preferably self pollinated.

As an alternative, the following protocol is used to produce herbicide resistant corn using a resistance gene of the present invention. Agrobacterium cells harboring the waterhemp herbicide resistance sequence of the present invention on a plasmid are grown in YP medium supplemented with appropriate antibiotics for 1-3 days. A loop of Agrobacterium cells is collected and suspended in 2 ml M-LS-002 medium (LS-inf) and the tube containing Agrobacterium cells is kept on a shaker for 1-3 hrs at 1,200 rpm.

Corncobs of genotype J553x(HIIIAxA188) are harvested at 7-12 days after pollination. The cobs are sterilized in a 20% Clorox solution for 15 min followed by thorough rinsing with sterile water. Immature embryos with size 0.8-2.0 mm are dissected into the tube containing Agrobacterium cells in LS-inf solution.

Agro-infection is carried out by keeping the tube horizontally in the laminar hood at room temperature for 30 min. The Agrobacterium infection mixture is poured on to a plate containing the co-cultivation medium (M-LS-011). After the liquid agro-solution is removed (using a pipette, for example), the embryos are plated on the co-cultivation medium with scutellum side up and cultured in the dark at 22° C. for 2-4 days.

Embryos are transferred to M-MS-101 medium without selection. Seven to ten days later, embryos are transferred to M-LS-401 medium containing 0.75 uM imazethapyr (or lactofen) and grown for 4 weeks to select for transformed callus cells.

Plant regeneration is initiated by transferring resistant calli to M-LS-504 medium supplemented with 0.75 μM imazethapyr (or lactofen) and grown under light at 26° C. for two to three weeks. Regenerated shoots are then transferred to a rooting box with M-MS-607 medium (0.5 μM imazethapyr or lactofen).

Plantlets with roots are transferred to potting mixture and grown in a growth chamber for a week, then transplanted to larger pots and maintained in a greenhouse till maturity.

Example 21 Production of Herbicide Tolerant Plants by Overexpression of PPO Sequences

The wild-type and the resistant waterhemp PPO coding sequences are excised by restriction endonuclease digestion and cloned into a suitable plant vector, for example, the binary vector pCIB200. These binary plasmids are transformed by electroporation into Agrobacterium and then into Arabidopsis thaliana using the vacuum infiltration method (Bechtold et al., 1993). Transformants are selected on kanamycin, and T2 seed is generated from a number of independent lines. This seed is plated on GM media containing various concentrations of PPO-inhibiting herbicide and scored for germination and survival. Multiple transgenic lines overexpressing either the wild type or the resistant mutant PPO enzyme produce significant numbers of green seedlings on an herbicide concentration that is lethal to the empty vector control.

Example 22 Production of Transgenic Herbicide Resistant Arabidopsis

Reverse transcription PCR (RT-PCR) products from resistant and sensitive biotypes were used as template for cloning the resistant and sensitive genes through PCR amplifications. These amplifications were performed using the ligation independent cloning (LIC) adapted oligonucleotide primers specific to PPX2L, P1 and P2, and cloned into the LIC site of a plant transformation vector, using techniques known to those skilled in the art. These primers used in these experiments were as follows: P1, TTGCTCTTCCATGGTAATTCAATCCATTAC, SEQ ID NO:49; P2, TTGCTCTTCGTTACGCGGTCTTCTCATCCATC, SEQ ID NO:50; P3, CATCGATCAAACTCGAGACCTCTGCCTCACTTTC, SEQ ID NO:51; P4, GAGGCAGAGGTCTCGAGTTTGATCGATGATCTTG, SEQ ID NO:52; P5, TTCACCAAGCTGTTTGCACATTGTGTCAACAAGTGTCT, SEQ ID NO:53; and P6, AGACACTTGTTGACACAATGTGCAAACAGCTTGGTGAA, SEQ ID NO:54. These plant transformation vectors contained an imidazolinone tolerant Arabidopsis AHAS large subunit gene under the control of the actin promoter and octopine synthase terminator, which allowed selection on Pursuit (imazethapyr) for all transformants, especially for selection of lactofen sensitive transformants. For expression of the resistant and sensitive genes in Arabidopsis, the coding sequences for each resistant or sensitive gene were inserted after the parsley ubiquitin promoter and before the nopaline synthase terminator. Several clones each of susceptible and resistant PPX2L were obtained from different biotype isolates and each was sequenced.

In addition, a chimeric “SRS” gene (see SEQ ID NO:45), which has the 5′ end of the susceptible coding sequence up to the unique XhoI site, the internal XhoI to DraIII fragment of the resistant coding sequence containing the resistance mutation, and the 3′ end of the susceptible from the unique DraIII site to the stop codon, was produced by amplifying sensitive RT-PCR template with P1 and P3 as well as with P6 and P2. Resistant template was also amplified with P4 and P5. These amplicons were digested with XhoI and DraIII and purified, then ligated. The ligation reaction was cloned into the LIC site of the plant transformation vector, as above.

Three vector plasmids were constructed: VC-MBW101-1, containing the susceptible version of the PPX2L gene (SEQ ID NO:47); VC-MBW102-1, containing the resistant version of the PPX2L gene (SEQ ID NO:25); and VC-MBW103-1, containing the SRS version of the PPX2L gene (SEQ ID NO:45); All three of these plasmids were transformed into Agrobacterium tumefaciens. as follows:

1-5 ng of the plasmid DNA isolated was transformed by electroporation into competent cells of Agrobacterium tumefaciens, of strain GV 3101 pMP90 (Koncz and Schell. 1986. Mol. Gen. Gent. 204:383-396). Thereafter, complete medium (YEP) was added and the mixture was transferred into a fresh reaction vessel for 3 hours at 28° C. Thereafter, all of the reaction mixture was plated onto YEP agar plates supplemented with the respective antibiotics, e.g. rifampicin (0.1 mg/ml), gentamicin (0.025 mg/ml and kanamycin (0.05 mg/ml) and incubated for 48 hours at 28° C. The agrobacterial cells containing the desired, relevant plasmid constructs were then used for the transformation of plants.

A colony was picked from the agar plate with the aid of a pipette tip and taken up in 3 ml of liquid TB medium, which also contained suitable antibiotics as described above. This preculture was grown for 48 hours at 28° C. and 120 rpm.

400 ml of LB medium containing the same antibiotics as above were used for the main culture. The preculture was transferred into the main culture. It was grown for 18 hours at 28° C. and 120 rpm. After centrifugation at 4 000 rpm, the pellet was resuspended in infiltration medium (MS medium, 10% sucrose).

In order to grow the plants for the transformation, dishes (Piki Saat 80, green, provided with a screen bottom, 30×20×4.5 cm, from Wiesauplast, Kunststofftechnik, DE) were half-filled with a GS 90 substrate (standard soil, Werkverband E.V., Germany). The dishes were watered overnight with 0.05% Proplant solution (Chimac-Apriphar, BE). Arabidopsis thaliana C24 seeds (Nottingham Arabidopsis Stock Centre, UK; NASC Stock N906) were scattered over the dish, approximately 1 000 seeds per dish. The dishes were covered with a hood and placed in the stratification facility (8 h, 110 μmol/m2/s-1, 22° C.; 16 h, dark, 6° C.). After 5 days, the dishes were placed into the short-day controlled environment chamber (8 h 130 μmol/m2/s-1, 22° C.; 16 h, dark 20° C.), where they remained for approximately 10 days until the first true leaves had formed.

The seedlings were transferred into pots containing the same substrate (Teku pots, 7 cm, LC series, manufactured by Poppelmann GmbH & Co, DE). Five plants were picked out into each pot. The pots were then returned into the short-day controlled environment chamber for the plant to continue growing.

After 10 days, the plants were transferred into the greenhouse cabinet (supplementary illumination, 16 h, 340 μE, 22° C.; 8 h, dark, 20° C.), where they were allowed to grow for further 17 days.

For the transformation, 6-week-old Arabidopsis plants, which had just started flowering were immersed for 10 seconds into the above-described agrobacterial suspension which had previously been treated with 10 μl Silwett L77 (Crompton S. A., Osi Specialties, CH). The method is described in Clough and Bent. 1998. Plant J. 16:735-743.

The plants were subsequently placed for 18 hours into a humid chamber. Thereafter, the pots were returned to the greenhouse for the plants to continue growing. The plants remained in the greenhouse for another 10 weeks until the seeds were ready for harvesting. Seeds harvested from these plants are the T1 seed generation.

These T1 generation seeds, which represented a collection of a few transformed seeds in a population of untransformed seeds, were sterilized by liquid sterilization (rinsing in a solution of 400 mL of ddH2O+100 mL of bleach+250 uL of 20% SDS, followed by rinsing in sterile distilled water).

These T1 seeds were put into 0.8% agarose and plated onto MS media with 1% sucrose, Cefotaxmine (500 ug/mL) and benomyl (2 ug/mL). For selection of transformants, these contained either 100 nM Pursuit (imazethapyr), 70 nM Cobra (lactofen) or 125 nM Cobra. Arabidopsis ecotype Columbia-0 (Co10) was also plated as a control on all types of plates and the imidazolinone tolerant mutant csr1-2 was plated on Pursuit plates as a positive control. The seeds were stratified on the plates for three days at 4° C.

The plates were then incubated in a Percival Scientific (Perry, Iowa) growth chamber at 21-22° C. and 15 hours of light for six days and scored for viable seedlings on the selective plates. The results are given in Table 18.

TABLE 18 Results of Plant Transformation Experiment. Seeds able to germinate on the herbicide-containing medium are those which contain and express the herbicide resistant PPX2L coding sequence. Calculated Number of Number of Germinated Number of Number of Number of Germinated Number of Seedlings per Seeds plated Germinated Seeds plated Seedlings on Germinated 1000 Seeds for T1 Seed on 70 nM Seedlings on on 125 nM 125 nM Seedlings on both rates of Description Lactofen 70 nM lactofen Lactofen Lactofen Imazethapyr Lactofen Columbia-0 884 0 600 0 0 0 (untransformed control) PPX2L Resistant 640 4 560 4 9 7 plasmid, transformation set 1 PPX2L Resistant 1276 3 1152 4 9 3 plasmid, transformation set 2 PPX2L Resistant 980 3 1664 1 6 2 plasmid, transformation set 3 PPX2L “SRS” 1176 14 1160 6 10 9 plasmid, transformation set 4-390 PPX2L “SRS” 1036 7 880 2 11 5 plasmid, transformation set 4-414 PPX2L Susceptible 500 0 680 0 4 0 plasmid, transformation set 4-291 PPX2L Susceptible 460 1 764 0 12 1 plasmid, transformation set 5

The numbers of seeds were the raw counts of actual seeds on the selection plates. The numbers of seedlings were the number of green seedlings found on each plate, indicative of resistance to the selective agent (lactofen or imazethapyr). If there were no seedlings, there were no resistant plants. Only the “resistant” forms of PPX2L conferred lactofen tolerance, confirming that the isolated PPX2L coding sequence from the herbicide resistant waterhemp was sufficient to confer the PPO-inhibiting herbicide resistance phenotype on transgenic plants into which the plant expressible sequence was introduced. The seed number for imazethapyr was not shown; rather, the seedling number from approximately 1000 seeds is indicated in the table. Plants obtained from the imazethapyr selection indicated the presence of transformed seeds with the sensitive form of PPX2L. Without wishing to be bound by any particular theory, the single seedling on transformation set 5 is believed to have been a stray resistant transformant. These data demonstrate that the resistant form of PPX2L conferred resistance to a PPO inhibiting herbicide, lactofen, to the transgenic plants expressing the resistant PPX2L.

Example 23 Genetic Engineering of Herbicide Resistant Tobacco

N. tabacum plant cells in culture are collected and prepared for biolistic transformation. Reference is made to the second sequence comparison in Table 20 herein above. One Glycine codon determining the underline Glycine pair is deleted in the sequence encoding this portion of the PPO protein which is embodied in the recombinagenic oligonucleotide. Particles are coated with recombinagenic oligonucleotide designed to introduce the herbicide resistance deletion mutation of the present in the PPO coding sequence, and they are introduced into the cells by biolistic transformation. Herbicide resistant cells are selected and cultured, and then plants are regenerated from those selected cells. Conventional screening and breeding techniques are employed to produce plants that are homozygous for this genetic trait. These plants can be used in improved production, in that treating with a PPO-inhibiting herbicide will not damage these plants, but will curtail the growth of herbicide sensitive weeds.

Example 24 Relationship of PPX2S and PPX2L

Segregation analysis was used to examine the genetic relationship between PPX2S and PPX2L. Total DNA was extracted from young leaf tissue using a modified hexadecyltrimethyl-ammonium bromide (CTAB) protocol as in Doyle and Doyle (1990). A fragment of PPX2 genomic DNA (gDNA) was amplified via polymerase chain reaction (PCR) using primers designed to amplify both PPX2S and PPX2L: PPX-CAPS-F, 5′-atgggcaacatttctgagcgg-3′ (SEQ ID NO:79), and PPX-CAPS-R, 5′-tgcctccagctctagaatcagctt-3′ (SEQ ID NO:80). PCRs contained about 100 ng total gDNA, 300 nM each of forward and reverse primers, 0.2 mM dNTPs, 2.5 mM MgCl₂, and 1 unit of Taq polymerase3 in 1×PCR buffer. The resulting product was digested with Fok14 to differentiate between PPX2S and PPX2L. The products were separated in 4% agarose gel containing 0.5 μg ml-1 ethidium bromide and visualized with ultraviolet light. A single nucleotide polymorphism (SNP) in PPX2S introduced an extra Fokl site in this gene. Using this marker, individuals from a herbicide-sensitive population from Wayne County, IL (WCS) (Patzoldt et al. 2006) were screened to identify plants testing positive for both PPX2S and PPX2L markers. A single male and multiple female plants with this genotype were allowed to cross. Two of the resultant F1 populations were tested for segregation of the SNP marker. Results were subjected to Chi-square analysis to determine if the results fit a single gene model.

Example 25 Sequencing 5′ End of PPX2

Sequence analysis of a gDNA fragment containing the 5′ end of PPX2 alleles was used to identify two in-frame start codons indicative of PPX2L. PCR was used to amplify this fragment from two WCS individuals, an individual from a herbicide-resistant population from Adams County, IL (ACR) (Patzoldt et al. 2006), and an F1 individual from the cross used for the PPX2 allele test that was determined to be homozygous for the PPX2S marker. PCRs were performed utilizing a primer designed from the 5′-UTR sequence of grain amaranth cv. ‘Plainsman’ (Amaranthus hypochondriacus L.) gDNA (provided by Jeff Maughan, Brigham Young University), PPX-5′-F, 5′-cacgttttgcacccaaacta-3′ (SEQ ID NO:81), in conjunction with PPX-CAPS-R (SEQ ID NO:80). PCR conditions were 2 minutes at 95 C followed by 37 cycles of 0.5 min at 95 C, 0.5 min at 55 C and 1.5 min at 72 C. The products were separated by gel electrophoresis then sequenced as described previously (Patzoldt et al. 2006).

Example 26 Testing Deletion-Specific PCR Marker

Inheritance of the ΔG210 PPX2L allele in F2 progeny from an ACR X WCS cross was studied by treating two replicates of 36 plants with 110 g ai ha-1 lactofen plus 1% COC. Fourteen DAT the plants were visually scored for herbicide damage. DNA was isolated from tissue samples taken prior to herbicide treatment. An allele-specific PCR marker was used to test for the presence of ΔG210. PCR with primers PPX2LR-F, 5′-tgttgcgggtacatgtgga-3′ (SEQ ID NO:82), and PPX2LR-R, 5′-tacttctggaaatgtatgg-3′ (SEQ ID NO:83), amplifies only the ΔG210 allele of PPX2L.

Products were fractionated in 2% agarose gel containing 0.5 μg ml-1 ethidium bromide and visualized with ultraviolet light. PCR assay data were compared to visual herbicide ratings. After this marker was tested on a segregating F2 population of known resistance mechanism, the assay was applied to other resistant populations where the resistance mechanism was unknown. Two replicates of six plants each from four suspected resistant populations and three sensitive populations were processed in the same manner as outlined for the F2 population.

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1. A method for producing a genetically engineered, non-transgenic, herbicide resistant or tolerant plant cell, said method comprising the steps of: (a) introducing into a plant cell a recombinagenic oligonucleotide with a targeted mutation in the protoporphyrin oxidase (PPO) gene to produce plant cells with a mutant PPO gene that expresses a mutant PPO protein that is deleted at an amino acid position corresponding to Gly210 or Gly 211 in the Amaranthus tuberculatus PPO protein or at an analogous amino acid residue in a PPO homolog; and (b) identifying a plant cell having a mutant PPO protein that has substantially the same catalytic activity as compared to a corresponding wild type PPO protein in the presence of herbicide except that said mutant PPO protein is not inhibited by the herbicide; and whereby a non-transgenic herbicide resistant plant cell is produced.
 2. The method of claim 1, wherein said herbicide resistant PPO is resistant to inhibition by lactofen, (±)-2-ethoxy-1-methyl-2-oxoethyl 5-{2-chloro-4-(trifluoromethyl)phenoxy}-2-nitrobenzoate; acifluorfen, 5-{2-chloro-4-(trifluoromethyl)phenoxy}-2-nitrobezoic acid; its methyl ester; or oxyfluorfen, 2-chloro-1-(3-ethoxy-4-nitrophenoxy)-4-(trifluorobenzene)}, oxidiazoles, (e.g., oxidiazon, 3-{2,4-dichloro-5-(1-methylethoxy)phenyl}-5-(1,1-dimethylethyl)-1,3,4-oxadiazol-2-(3H)-one), cyclic imides (e.g., S-23142, N-(4-chloro-2-fluoro-5-propargyloxyphenyl)-3,4,5,6-tetrahydrophthalimide; chlorophthalim, N-(4-chlorophenyl)-3,4,5,6-tetrahydrophthalimide), phenyl pyrazoles (e.g. TNPP-ethyl, ethyl 2-{1-(2,3,4-trichlorophenyl)-4-nitropyrazolyl-5-oxy}propionate; M&B 39279), pyridine derivatives (e.g. LS 82-556), phenopylate and O-phenylpyrrolidino- and piperidinocarbamate analogs thereof, and 3-phenyluracils of formula I

wherein R¹ is methyl or NH₂; R² is C₁-C₂-haloalkyl; R³ is hydrogen or halogen; R⁴ is halogen or cyano; R⁵ is hydrogen, cyano, C₁-C₆-alkyl, C₁-C₆-alkoxy, C₁-C₄-alkoxy-C₁-C₄-alkyl, C₃-C₇-cycloalkyl, C₃-C₆-alkenyl, C₃-C₆-alkynyl or benzyl which is unsubstituted or substituted by halogen or alkyl; and R⁶, R⁷ independently of one another are hydrogen, C₁-C₆-alkyl, C₁-C₆-alkoxy, C₃-C₆-alkenyl, C₃-C₆-alkynyl, C₃-C₇-cycloalkyl, C₃-C₇-cycloalkenyl, phenyl or benzyl, where each of the 8 abovementioned substituents is unsubstituted or may be substituted by 1 to 6 halogen atoms and/or by one, two or three groups selected from: OH, NH₂, CN, CONH₂, C₁-C₄-alkoxy, C₁-C₄-haloalkoxy, C₁-C₄-alkylthio, C₁-C₄-haloalkylthio, C₁-C₄-alkylsulfonyl, C₁-C₄-haloalkylsulfonyl, C₁-C₄-alkylamino, di(C₁-C₄-alkyl)amino, formyl, C₁-C₄-alkylcarbonyl, C₁-C₄-alkoxycarbonyl, C₁-C₄-alkylaminocarbonyl, di(C₁-C₄-alkyl)aminocarbonyl, C₃-C₇-cycloalkyl, phenyl and benzyl; or R⁶, R⁷ together with the nitrogen atom form a 3-, 4-, 5-, 6- or 7-membered saturated or unsaturated nitrogen heterocycle which may be substituted by 1 to 6 methyl groups and which may contain 1 or 2 further heteroatoms selected from the group consisting of nitrogen, oxygen and sulfur as ring members.
 3. The method according to claim 1 wherein the recombinagenic oligonucleotide is a mixed duplex nucleotide which contains a first homologous region which has a sequence identical to the sequence of at least 6 base pairs of the first fragment of the target PPO gene and a second homologous region which has a sequence identical to the sequence of at least 6 base pairs of a second fragment of the target PPO gene, and an intervening region which contains at least one nucleobase heterologous to the target PPO gene, which intervening region connects the first and second homologous region.
 4. The method according to claim 1 in which the recombinagenic oligonucleotide is introduced by electroporation, biolistic transformation or polyethylene glycol precipitation.
 5. The method of claim 1, further comprising after step (b), (c) regenerating a plant having a mutated PPO gene from said plant cell, whereby a non-transgenic herbicide resistant plant is produced.
 6. The method according to claim 1 in which the amino acid deletion is in a corn, wheat, rice, barley, soybean, cotton, sugarbeet, oilseed rape, canola, flax, sunflower, potato, tobacco, tomato, alfalfa, poplar, pine, eucalyptus, apple, lettuce, pea, lentil, grape, turf grass, Brassica or Arabidopsis thaliana homolog of the PPO of Amaranthus tuberculatus as set forth in SEQ ID NO:16.
 7. A plant, progeny plant, plant cell, plant tissue or seed of the plant produced by the method of claim 5, wherein said progeny plant, cell, tissue or seed contains within its genetic complement the mutant PPO gene that expresses a mutant PPO protein that is deleted at an amino acid position corresponding to Gly210 or Gly 211 in the Amaranthus tuberculatus PPO protein or at an analogous amino acid residue in a PPO homolog.
 8. The plant, plant cell or plant tissue of claim 7, which is or is from a dicotyledonous plant.
 9. The plant, plant cell or plant tissue of claim 8, which is or is from Arabidopsis, cotton, sunflower, cabbage, broccoli, cauliflower, Brussels sprout, canola, bean, pea, soybean, citrus, tomato, potato, sweet potato, plum, peach, apple, pear, cherry, grape, rose, tobacco, alfalfa, trefoil, sugar beet, blackberry, raspberry, blueberry, marionberry, loganberry, apricot, eggplant, pepper, pumpkin, squash, gourd, an ornamental plant, aspen, poplar, maple, oak, sunflower, rose or tobacco.
 10. The plant, plant cell or plant tissue of claim 7, which is or is from a monocotyledonous plant.
 11. The plant, plant cell or plant tissue of claim 10, which is or is from wheat, corn, rice, sorghum, oat, wild rice, barley, millet or turfgrass.
 12. A method of controlling weeds comprising the step of planting a non-transgenic, genetically engineered, herbicide resistant plant, plant, progeny plant or seed containing within its genetic complement the mutant PPO gene that expresses a mutant PPO protein that is deleted at an amino acid position corresponding to Gly210 or Gly 211 in the Amaranthus tuberculatus PPO protein or at an analogous amino acid residue in a PPO homolog; and treating the plants with a herbicide to which resistance is conferred by said molecule, whereby growth of weeds is controlled.
 13. A method of selecting a non-transgenic, genetically engineered, herbicide resistant plant cell or plant tissue containing within its genetic complement the mutant PPO gene that expresses a mutant PPO protein that is deleted at an amino acid position corresponding to Gly210 or Gly 211 in the Amaranthus tuberculatus PPO protein or at an analogous amino acid residue in a PPO homolog, said method comprising the steps of growing said plant cell or plant tissue on a medium comprising an amount of an inhibitor of protoporphoryinogen oxidase sufficient to prevent growth of a corresponding plant cell which does not contain and express said nucleic acid molecule. 